🔍 Code Extractor

Manages extraction and formatting of references for LLM chat responses. Handles both file references and BibTeX citations, formatting them according to various academic citation styles.

Purpose

Manages extraction and formatting of references for LLM chat responses. Handles both file references and BibTeX citations, formatting them according to various academic citation styles.

Source Code

class ReferenceManager:
    """
    Manages extraction and formatting of references for LLM chat responses.
    Handles both file references and BibTeX citations, formatting them according
    to various academic citation styles.
    """
    
    def __init__(self, default_style="apa"):
        """
        Initialize the reference manager.
        
        Args:
            default_style: Default citation style to use
        """
        self.default_style = default_style
        self.style_titles = {
            "apa": "References",
            "mla": "Works Cited",
            "chicago": "Bibliography",
            "ieee": "References",
            "harvard1": "References",
            "vancouver": "References",
            "nature": "References"
        }

    
    
    def extract_references(self, text):
        """
        Extract block references from text in various formats including:
        - Single blocks: [block X] or [Block X]
        - Multiple blocks: [Block X, Block Y, Block Z] or [Block X, Y, Z]
        
        Args:
            text: Text to extract references from
            
        Returns:
            list: List of block numbers referenced in the text
        """
        # Regex patterns to find different reference formats
        # Single block pattern: [block 1] or [Block 1]
        single_pattern = r'\[(?:[Bb]lock)\s+(\d+)\]'
        # Multiple blocks pattern: [Block 1, Block 2, Block 3]
        multi_block_pattern = r'\[(?:[Bb]lock\s+\d+(?:,\s*[Bb]lock\s+\d+)+)\]'
        # Multiple blocks pattern with abbreviated format: [Block 1, 2, 3]
        abbreviated_pattern = r'\[(?:[Bb]lock\s+\d+(?:,\s*\d+)+)\]'
        
        # Find all patterns and extract block numbers
        unique_refs = []
        
        # Extract single block references
        single_refs = re.findall(single_pattern, text)
        for ref in single_refs:
            block_num = int(ref)
            if block_num not in unique_refs:
                unique_refs.append(block_num)
        
        # Extract multiple block references with full "Block X" format
        multi_blocks = re.findall(multi_block_pattern, text)
        for block_group in multi_blocks:
            # Remove outer brackets
            clean_group = block_group[1:-1]
            # Find all block numbers in this group
            block_nums = re.findall(r'[Bb]lock\s+(\d+)', clean_group)
            for num in block_nums:
                block_num = int(num)
                if block_num not in unique_refs:
                    unique_refs.append(block_num)
        
        # Extract multiple block references with abbreviated format
        abbreviated_blocks = re.findall(abbreviated_pattern, text)
        for block_group in abbreviated_blocks:
            # Remove outer brackets
            clean_group = block_group[1:-1]
            # Find the first block number (with "Block" prefix)
            first_block_match = re.search(r'[Bb]lock\s+(\d+)', clean_group)
            if first_block_match:
                first_block = int(first_block_match.group(1))
                if first_block not in unique_refs:
                    unique_refs.append(first_block)
                
                # Find all additional numbers in this group
                additional_nums = re.findall(r',\s*(\d+)', clean_group)
                for num in additional_nums:
                    block_num = int(num)
                    if block_num not in unique_refs:
                        unique_refs.append(block_num)
        
        return unique_refs
    
    def process_references(self, text, blocks_dict, style=None):
        """
        Process references in text, lookup block information, and generate reference section.
        
        Args:
            text: Text containing references
            blocks_dict: Dictionary with block data indexed by block number
            style: Citation style to use (defaults to self.default_style)
            
        Returns:
            tuple: (updated_text, references_section)
        """
        # Use default style if none specified
        if style is None:
            style = self.default_style
            
        # Extract referenced block numbers
        block_numbers = self.extract_references(text)
        #print("block numbers", block_numbers)
        
        if not block_numbers:
            return text, ""  # No references found
            
        # Prepare reference objects
        references = []
        citation_map = {}
        
        for i, block_num in enumerate(block_numbers, 1):
            if block_num not in blocks_dict:
                continue  # Skip if block not found
                
            block_data = blocks_dict[block_num]
            #print("block data", block_data)
            block_type = block_data.get("type", "unknown")
            ref_id = str(i)
            
            
            # Create reference object based on block type
            if block_type == "document":
                # Document/file reference
                ref_obj = {
                    "id": ref_id,
                    "type": "file",
                    "path": block_data.get("path", ""),
                    "description": block_data.get("description", None)
                }
            elif block_type == "literature":
                # BibTeX reference
                ref_obj = {
                    "id": ref_id,
                    "type": "bibtex",
                    "content": block_data.get("bibtex", "")
                }
            elif block_type == "web":
                # Web reference
                ref_obj = {
                    "id": ref_id,
                    "type": "web",
                    "url": block_data.get("url", ""),
                    "title": block_data.get("title", "Web Page"),
                    "snippet": block_data.get("snippet", ""),
                    "date": block_data.get("date", "")
                }
            else:
                # Generic reference (fallback)
                ref_obj = {
                    "id": ref_id,
                    "type": "generic",
                    "content": block_data.get("content", "")
                }
                
            references.append(ref_obj)
            citation_map[block_num] = ref_id
            
        # Generate reference section
        references_section, _ = self.generate_references_section(references, style)
        
        # Replace [block X] references with [N] citation format
        updated_text = text
        
        # First, handle standard single block references like [Block 1] or [block 1]
        for block_num, ref_id in citation_map.items():
            updated_text = updated_text.replace(f"[block {block_num}]", f"[{ref_id}]")
            updated_text = updated_text.replace(f"[Block {block_num}]", f"[{ref_id}]")
        
        # Handle complex multi-block references like [Block 1, Block 2, Block 3]
        # by looking for all block references and replacing them one by one
        multi_block_refs = re.findall(r'\[(?:[Bb]lock\s+\d+(?:,\s*(?:[Bb]lock\s+)?\d+)*)\]', updated_text)
        for ref_group in multi_block_refs:
            new_ref = ref_group
            for block_num, ref_id in citation_map.items():
                # Replace full "Block X" and "block X" patterns
                new_ref = new_ref.replace(f"Block {block_num}", f"{ref_id}")
                new_ref = new_ref.replace(f"block {block_num}", f"{ref_id}")
                
                # Also replace just the number when in a list context (preceded by comma and spaces)
                new_ref = re.sub(r',\s*' + str(block_num) + r'(?=[\s,\]])', f', {ref_id}', new_ref)
            
            # Fix the format to remove any "Block" text that's left
            new_ref = re.sub(r'[Bb]lock\s+', '', new_ref)
            
            # Clean up spaces and commas
            new_ref = re.sub(r'\s+', ' ', new_ref)  # Normalize whitespace
            new_ref = re.sub(r',\s*,', ',', new_ref)  # Remove double commas
            new_ref = re.sub(r'^\[(,\s*)+', '[', new_ref)  # Clean start of reference
            
            # Replace the original reference group with the new one
            updated_text = updated_text.replace(ref_group, new_ref)
        
        return updated_text, references_section
    
    def format_bibtex_reference(self, bibtex_string, ref_id, style_name="apa"):
        """
        Format a BibTeX entry.
        
        Args:
            bibtex_string: BibTeX entry as a string
            ref_id: Reference ID for citation
            style_name: Style name (apa, ieee, etc.)
            
        Returns:
            tuple: (citation_marker, reference_entry)
        """
        # Parse BibTeX string
        parser = bibtex.Parser()
        bib_data = parser.parse_string(bibtex_string)
        
        # Get the key of the first entry
        entry_key = list(bib_data.entries)[0]
        entry = bib_data.entries[entry_key]
        
        # Create citation marker
        citation_marker = f"[{ref_id}]"
        
        # Extract common fields
        authors = self.format_authors(entry, style_name)
        title = entry.fields.get('title', '')
        journal = entry.fields.get('journal', '')
        year = entry.fields.get('year', '')
        volume = entry.fields.get('volume', '')
        number = entry.fields.get('number', '')
        pages = entry.fields.get('pages', '')
        month = entry.fields.get('month', '')
        doi = entry.fields.get('doi', '')
        publisher = entry.fields.get('publisher', '')
        address = entry.fields.get('address', '')
        
        # Format according to style and entry type
        if entry.type == 'article':
            if style_name.lower() == "apa":
                # APA: Author. (Year). Title. Journal, Volume(Number), Pages.
                reference = f"{authors} ({year}). {title}. *{journal}*, {volume}"
                if number:
                    reference += f"({number})"
                reference += f", {pages}."
                
            elif style_name.lower() == "ieee":
                # IEEE: Author, "Title," Journal, vol. Volume, no. Number, pp. Pages, Month Year.
                reference = f"{authors}, \"{title},\" *{journal}*"
                if volume:
                    reference += f", vol. {volume}"
                if number:
                    reference += f", no. {number}"
                reference += f", pp. {pages}"
                if month:
                    reference += f", {month}"
                reference += f" {year}."
                
            elif style_name.lower() == "chicago":
                # Chicago: Author. "Title." Journal Volume, no. Number (Year): Pages.
                reference = f"{authors}. \"{title}.\" *{journal}* {volume}"
                if number:
                    reference += f", no. {number}"
                reference += f" ({year}): {pages}."
                
            elif style_name.lower() == "nature":
                # Nature: Author. Title. Journal Volume, Pages (Year).
                reference = f"{authors}. {title}. *{journal}* {volume}, {pages} ({year})."
                
            elif style_name.lower() == "harvard1":
                # Harvard: Author (Year) 'Title', Journal, Volume(Number), pp. Pages.
                reference = f"{authors} ({year}) '{title}', *{journal}*, {volume}"
                if number:
                    reference += f"({number})"
                reference += f", pp. {pages}."
                
            elif style_name.lower() == "vancouver":
                # Vancouver: Author. Title. Journal. Year;Volume(Number):Pages.
                reference = f"{authors}. {title}. {journal}. {year};{volume}"
                if number:
                    reference += f"({number})"
                reference += f":{pages}."
                
            else:
                # Plain: Author. Title. Journal, Volume(Number), Pages, Year.
                reference = f"{authors}. {title}. *{journal}*, {volume}"
                if number:
                    reference += f"({number})"
                reference += f", {pages}, {year}."
                
        elif entry.type in ['book', 'incollection', 'inbook']:
            if style_name.lower() == "apa":
                # APA: Author. (Year). Title. Publisher, Address.
                reference = f"{authors} ({year}). *{title}*. "
                if publisher:
                    reference += f"{publisher}"
                    if address:
                        reference += f", {address}"
                reference += "."
                
            elif style_name.lower() == "ieee":
                # IEEE: Author, Title. Address: Publisher, Year.
                reference = f"{authors}, *{title}*"
                if address or publisher:
                    reference += ". "
                    if address:
                        reference += f"{address}"
                        if publisher:
                            reference += ": "
                    if publisher:
                        reference += f"{publisher}"
                reference += f", {year}."
                
            elif style_name.lower() == "chicago":
                # Chicago: Author. Title. Address: Publisher, Year.
                reference = f"{authors}. *{title}*. "
                if address:
                    reference += f"{address}: "
                if publisher:
                    reference += f"{publisher}, "
                reference += f"{year}."
                
            else:
                # Default/Plain: Author. Title. Publisher, Address, Year.
                reference = f"{authors}. *{title}*. "
                if publisher:
                    reference += f"{publisher}"
                    if address:
                        reference += f", {address}"
                reference += f", {year}."
        
        else:  # Other entry types
            # Generic format for misc entry types
            reference = f"{authors} ({year}). {title}."
        
        # Add DOI with proper Markdown link formatting if available
        if doi and "doi:" not in reference.lower() and "doi.org" not in reference.lower():
            reference += f" [doi:{doi}](https://doi.org/{doi})"
        
        # Format as a numbered reference
        markdown_reference = f"[{ref_id}]: {reference}"
        
        return citation_marker, markdown_reference

    def format_authors(self, entry, style_name):
        """Format authors according to the style."""
        if 'author' not in entry.persons and 'editor' not in entry.persons:
            return ""
        
        # Use editors if no authors are available
        if 'author' in entry.persons:
            authors = entry.persons['author']
        else:
            authors = entry.persons['editor']
            
        # IEEE, Vancouver: Use last name first with initials
        if style_name.lower() in ["ieee", "vancouver"]:
            if len(authors) == 1:
                return self.format_last_first(authors[0], True)
            elif len(authors) <= 7:
                names = [self.format_last_first(author, True) for author in authors[:-1]]
                names.append(f"and {self.format_last_first(authors[-1], True)}")
                return ", ".join(names)
            else:
                # More than 7 authors: show first 6 + et al.
                names = [self.format_last_first(author, True) for author in authors[:6]]
                names.append("et al.")
                return ", ".join(names)
        
        # Harvard, APA: Normal order with full first names, et al. for >3
        elif style_name.lower() in ["harvard1", "apa"]:
            if len(authors) > 7:
                # For APA with more than 7 authors: First 6 + ... + last author
                names = [self.format_name(author) for author in authors[:6]]
                names.append("...")
                names.append(self.format_name(authors[-1]))
                return ", ".join(names)
            elif len(authors) > 3:
                return f"{self.format_name(authors[0])} et al."
            elif len(authors) == 1:
                return self.format_name(authors[0])
            else:
                names = [self.format_name(author) for author in authors[:-1]]
                names.append(f"and {self.format_name(authors[-1])}")
                return ", ".join(names)
        
        # Nature: All authors in normal order
        elif style_name.lower() == "nature":
            if len(authors) == 1:
                return self.format_name(authors[0])
            else:
                names = [self.format_name(author) for author in authors[:-1]]
                names.append(f"& {self.format_name(authors[-1])}")
                return ", ".join(names)
        
        # Chicago: All authors in normal order
        elif style_name.lower() == "chicago":
            if len(authors) == 1:
                return self.format_name(authors[0])
            else:
                names = [self.format_name(author) for author in authors[:-1]]
                names.append(f"and {self.format_name(authors[-1])}")
                return ", ".join(names)
        
        # Default: Normal order
        else:
            if len(authors) == 1:
                return self.format_name(authors[0])
            else:
                names = [self.format_name(author) for author in authors[:-1]]
                names.append(f"and {self.format_name(authors[-1])}")
                return ", ".join(names)

    def format_name(self, person):
        """Format a person's name in normal order: First Middle Last"""
        first = " ".join(person.first_names)
        last = " ".join(person.last_names)
        return f"{first} {last}"
        
    def format_last_first(self, person, initials=False):
        """Format a person's name as Last, First or Last, F."""
        if initials:
            first = " ".join([name[0] + "." for name in person.first_names])
        else:
            first = " ".join(person.first_names)
        
        last = " ".join(person.last_names)
        
        if first:
            return f"{last}, {first}"
        else:
            return last

    def process_web_reference(self, web_data, ref_id):
        """
        Convert a web reference to a formatted citation according to style.
        
        Args:
            web_data: Dictionary with web reference data (title, url, etc.)
            ref_id: Reference ID for citation
            
        Returns:
            tuple: (citation_marker, reference_entry)
        """
        citation_marker = f"[{ref_id}]"
        
        # Extract web data
        title = web_data.get("title", "Web Page")
        url = web_data.get("url", "")
        date = web_data.get("date", "")
        
        # If no date is provided, use current date
        if not date:
            from datetime import datetime
            date = datetime.now().strftime("%B %d, %Y")
        
        # Format according to APA style for websites
        markdown_reference = f"[{ref_id}] {title}. "
        
        # Add date if available
        if date:
            markdown_reference += f"({date}). "
        
        # Add URL
        markdown_reference += f"Retrieved from [{url}]({url})"
        
        return citation_marker, markdown_reference

    def process_file_reference(self, filepath, ref_id, description=None):
        """
        Convert a filepath to a markdown reference with clickable link.
        
        Args:
            filepath: Path to the file
            ref_id: Reference ID for citation
            description: Optional description for the file
            
        Returns:
            tuple: (citation_marker, reference_entry)
        """
        citation_marker = f"[{ref_id}]"
        
        # Create file basename for display
        filename = os.path.basename(filepath)
        
        # Create clickable URL in the specific format:
        # https://filecloud.vicebio.com/ui/core/index.html?filter=FILENAME#expl-tabl.%2FSHARED%2Fvicebio_shares%2FPATH
        
        # Escape spaces in filename with + for the first part
        encoded_filename = filename.replace(' ', '+')
        
        # Encode path for the second part (after #expl-tabl.)
        # Extract directory path without filename
        directory_path = os.path.dirname(filepath)
        # Ensure path ends with '/'
        if directory_path and not directory_path.endswith('/'):
            directory_path += '/'
        
        encoded_path = f"/SHARED/vicebio_shares/{directory_path}"
        encoded_path = encoded_path.replace(' ', '%20')
        
        # Construct the full URL
        file_url = f"https://filecloud.vicebio.com/ui/core/index.html?filter={encoded_filename}#expl-tabl.{encoded_path}"
        
        # Create the reference with description if provided
        if description:
            markdown_reference = f"[{ref_id}]: **{description}**: [{filename}]({file_url})"
        else:
            markdown_reference = f"[{ref_id}]: [{filename}]({file_url})"
        
        return citation_marker, markdown_reference

    def generate_references_section(self, references, style="apa"):
        """
        Generate a complete references section in Markdown from a list of reference objects.
        
        Args:
            references: List of reference objects (dictionaries with required fields)
            style: Citation style to use (e.g., 'apa', 'ieee', 'nature', etc.)
            
        Returns:
            tuple: (markdown_output, citation_map)
        """
        title = self.style_titles.get(style.lower(), "References")
        markdown_output = f"## {title}\n\n"
        citation_map = {}
        
        # Format each reference
        for ref in references:
            ref_id = ref["id"]
            ref_type = ref["type"]
            
            if ref_type == "bibtex":
                citation, reference = self.format_bibtex_reference(ref["content"], ref_id, style)
            elif ref_type == "file" or ref_type == "document":
                description = ref.get("description", None)
                citation, reference = self.process_file_reference(ref["path"], ref_id, description)
            elif ref_type == "web":
                citation, reference = self.process_web_reference(ref, ref_id)
            else:
                # Simple text reference
                citation_marker = f"[{ref_id}]"
                markdown_reference = f"[{ref_id}]: {ref.get('content', 'Reference')}"
                citation, reference = citation_marker, markdown_reference
                
            markdown_output += reference + "\n\n"
            citation_map[ref_id] = citation
        
        return markdown_output.strip(), citation_map

    def list_available_styles(self):
        """
        List all available citation styles
        
        Returns:
            list: Names of available styles
        """
        return ["apa", "ieee", "chicago", "harvard1", "nature", "vancouver", "plain"]

Parameters

Name	Type	Default	Kind
bases	-	-

Parameter Details

bases: Parameter of type

Return Value

Returns unspecified type

Class Interface

Methods

Required Imports

from typing import List
from typing import Any
from typing import Dict
import os
import panel as pn

Usage Example

# Example usage:
# result = ReferenceManager(bases)

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class ReferenceManager:
    """
    Manages extraction and formatting of references for LLM chat responses.
    Handles both file references and BibTeX citations, formatting them according
    to various academic citation styles.
    """
    
    def __init__(self, default_style="apa"):
        """
        Initialize the reference manager.
        
        Args:
            default_style: Default citation style to use
        """
        self.default_style = default_style
        self.style_titles = {
            "apa": "References",
            "mla": "Works Cited",
            "chicago": "Bibliography",
            "ieee": "References",
            "harvard1": "References",
            "vancouver": "References",
            "nature": "References"
        }

    
    
    def extract_references(self, text):
        """
        Extract block references from text in various formats including:
        - Single blocks: [block X] or [Block X]
        - Multiple blocks: [Block X, Block Y, Block Z] or [Block X, Y, Z]
        
        Args:
            text: Text to extract references from
            
        Returns:
            list: List of block numbers referenced in the text
        """
        # Regex patterns to find different reference formats
        # Single block pattern: [block 1] or [Block 1]
        single_pattern = r'\[(?:[Bb]lock)\s+(\d+)\]'
        # Multiple blocks pattern: [Block 1, Block 2, Block 3]
        multi_block_pattern = r'\[(?:[Bb]lock\s+\d+(?:,\s*[Bb]lock\s+\d+)+)\]'
        # Multiple blocks pattern with abbreviated format: [Block 1, 2, 3]
        abbreviated_pattern = r'\[(?:[Bb]lock\s+\d+(?:,\s*\d+)+)\]'
        
        # Find all patterns and extract block numbers
        unique_refs = []
        
        # Extract single block references
        single_refs = re.findall(single_pattern, text)
        for ref in single_refs:
            block_num = int(ref)
            if block_num not in unique_refs:
                unique_refs.append(block_num)
        
        # Extract multiple block references with full "Block X" format
        multi_blocks = re.findall(multi_block_pattern, text)
        for block_group in multi_blocks:
            # Remove outer brackets
            clean_group = block_group[1:-1]
            # Find all block numbers in this group
            block_nums = re.findall(r'[Bb]lock\s+(\d+)', clean_group)
            for num in block_nums:
                block_num = int(num)
                if block_num not in unique_refs:
                    unique_refs.append(block_num)
        
        # Extract multiple block references with abbreviated format
        abbreviated_blocks = re.findall(abbreviated_pattern, text)
        for block_group in abbreviated_blocks:
            # Remove outer brackets
            clean_group = block_group[1:-1]
            # Find the first block number (with "Block" prefix)
            first_block_match = re.search(r'[Bb]lock\s+(\d+)', clean_group)
            if first_block_match:
                first_block = int(first_block_match.group(1))
                if first_block not in unique_refs:
                    unique_refs.append(first_block)
                
                # Find all additional numbers in this group
                additional_nums = re.findall(r',\s*(\d+)', clean_group)
                for num in additional_nums:
                    block_num = int(num)
                    if block_num not in unique_refs:
                        unique_refs.append(block_num)
        
        return unique_refs
    
    def process_references(self, text, blocks_dict, style=None):
        """
        Process references in text, lookup block information, and generate reference section.
        
        Args:
            text: Text containing references
            blocks_dict: Dictionary with block data indexed by block number
            style: Citation style to use (defaults to self.default_style)
            
        Returns:
            tuple: (updated_text, references_section)
        """
        # Use default style if none specified
        if style is None:
            style = self.default_style
            
        # Extract referenced block numbers
        block_numbers = self.extract_references(text)
        #print("block numbers", block_numbers)
        
        if not block_numbers:
            return text, ""  # No references found
            
        # Prepare reference objects
        references = []
        citation_map = {}
        
        for i, block_num in enumerate(block_numbers, 1):
            if block_num not in blocks_dict:
                continue  # Skip if block not found
                
            block_data = blocks_dict[block_num]
            #print("block data", block_data)
            block_type = block_data.get("type", "unknown")
            ref_id = str(i)
            
            
            # Create reference object based on block type
            if block_type == "document":
                # Document/file reference
                ref_obj = {
                    "id": ref_id,
                    "type": "file",
                    "path": block_data.get("path", ""),
                    "description": block_data.get("description", None)
                }
            elif block_type == "literature":
                # BibTeX reference
                ref_obj = {
                    "id": ref_id,
                    "type": "bibtex",
                    "content": block_data.get("bibtex", "")
                }
            elif block_type == "web":
                # Web reference
                ref_obj = {
                    "id": ref_id,
                    "type": "web",
                    "url": block_data.get("url", ""),
                    "title": block_data.get("title", "Web Page"),
                    "snippet": block_data.get("snippet", ""),
                    "date": block_data.get("date", "")
                }
            else:
                # Generic reference (fallback)
                ref_obj = {
                    "id": ref_id,
                    "type": "generic",
                    "content": block_data.get("content", "")
                }
                
            references.append(ref_obj)
            citation_map[block_num] = ref_id
            
        # Generate reference section
        references_section, _ = self.generate_references_section(references, style)
        
        # Replace [block X] references with [N] citation format
        updated_text = text
        
        # First, handle standard single block references like [Block 1] or [block 1]
        for block_num, ref_id in citation_map.items():
            updated_text = updated_text.replace(f"[block {block_num}]", f"[{ref_id}]")
            updated_text = updated_text.replace(f"[Block {block_num}]", f"[{ref_id}]")
        
        # Handle complex multi-block references like [Block 1, Block 2, Block 3]
        # by looking for all block references and replacing them one by one
        multi_block_refs = re.findall(r'\[(?:[Bb]lock\s+\d+(?:,\s*(?:[Bb]lock\s+)?\d+)*)\]', updated_text)
        for ref_group in multi_block_refs:
            new_ref = ref_group
            for block_num, ref_id in citation_map.items():
                # Replace full "Block X" and "block X" patterns
                new_ref = new_ref.replace(f"Block {block_num}", f"{ref_id}")
                new_ref = new_ref.replace(f"block {block_num}", f"{ref_id}")
                
                # Also replace just the number when in a list context (preceded by comma and spaces)
                new_ref = re.sub(r',\s*' + str(block_num) + r'(?=[\s,\]])', f', {ref_id}', new_ref)
            
            # Fix the format to remove any "Block" text that's left
            new_ref = re.sub(r'[Bb]lock\s+', '', new_ref)
            
            # Clean up spaces and commas
            new_ref = re.sub(r'\s+', ' ', new_ref)  # Normalize whitespace
            new_ref = re.sub(r',\s*,', ',', new_ref)  # Remove double commas
            new_ref = re.sub(r'^\[(,\s*)+', '[', new_ref)  # Clean start of reference
            
            # Replace the original reference group with the new one
            updated_text = updated_text.replace(ref_group, new_ref)
        
        return updated_text, references_section
    
    def format_bibtex_reference(self, bibtex_string, ref_id, style_name="apa"):
        """
        Format a BibTeX entry.
        
        Args:
            bibtex_string: BibTeX entry as a string
            ref_id: Reference ID for citation
            style_name: Style name (apa, ieee, etc.)
            
        Returns:
            tuple: (citation_marker, reference_entry)
        """
        # Parse BibTeX string
        parser = bibtex.Parser()
        bib_data = parser.parse_string(bibtex_string)
        
        # Get the key of the first entry
        entry_key = list(bib_data.entries)[0]
        entry = bib_data.entries[entry_key]
        
        # Create citation marker
        citation_marker = f"[{ref_id}]"
        
        # Extract common fields
        authors = self.format_authors(entry, style_name)
        title = entry.fields.get('title', '')
        journal = entry.fields.get('journal', '')
        year = entry.fields.get('year', '')
        volume = entry.fields.get('volume', '')
        number = entry.fields.get('number', '')
        pages = entry.fields.get('pages', '')
        month = entry.fields.get('month', '')
        doi = entry.fields.get('doi', '')
        publisher = entry.fields.get('publisher', '')
        address = entry.fields.get('address', '')
        
        # Format according to style and entry type
        if entry.type == 'article':
            if style_name.lower() == "apa":
                # APA: Author. (Year). Title. Journal, Volume(Number), Pages.
                reference = f"{authors} ({year}). {title}. *{journal}*, {volume}"
                if number:
                    reference += f"({number})"
                reference += f", {pages}."
                
            elif style_name.lower() == "ieee":
                # IEEE: Author, "Title," Journal, vol. Volume, no. Number, pp. Pages, Month Year.
                reference = f"{authors}, \"{title},\" *{journal}*"
                if volume:
                    reference += f", vol. {volume}"
                if number:
                    reference += f", no. {number}"
                reference += f", pp. {pages}"
                if month:
                    reference += f", {month}"
                reference += f" {year}."
                
            elif style_name.lower() == "chicago":
                # Chicago: Author. "Title." Journal Volume, no. Number (Year): Pages.
                reference = f"{authors}. \"{title}.\" *{journal}* {volume}"
                if number:
                    reference += f", no. {number}"
                reference += f" ({year}): {pages}."
                
            elif style_name.lower() == "nature":
                # Nature: Author. Title. Journal Volume, Pages (Year).
                reference = f"{authors}. {title}. *{journal}* {volume}, {pages} ({year})."
                
            elif style_name.lower() == "harvard1":
                # Harvard: Author (Year) 'Title', Journal, Volume(Number), pp. Pages.
                reference = f"{authors} ({year}) '{title}', *{journal}*, {volume}"
                if number:
                    reference += f"({number})"
                reference += f", pp. {pages}."
                
            elif style_name.lower() == "vancouver":
                # Vancouver: Author. Title. Journal. Year;Volume(Number):Pages.
                reference = f"{authors}. {title}. {journal}. {year};{volume}"
                if number:
                    reference += f"({number})"
                reference += f":{pages}."
                
            else:
                # Plain: Author. Title. Journal, Volume(Number), Pages, Year.
                reference = f"{authors}. {title}. *{journal}*, {volume}"
                if number:
                    reference += f"({number})"
                reference += f", {pages}, {year}."
                
        elif entry.type in ['book', 'incollection', 'inbook']:
            if style_name.lower() == "apa":
                # APA: Author. (Year). Title. Publisher, Address.
                reference = f"{authors} ({year}). *{title}*. "
                if publisher:
                    reference += f"{publisher}"
                    if address:
                        reference += f", {address}"
                reference += "."
                
            elif style_name.lower() == "ieee":
                # IEEE: Author, Title. Address: Publisher, Year.
                reference = f"{authors}, *{title}*"
                if address or publisher:
                    reference += ". "
                    if address:
                        reference += f"{address}"
                        if publisher:
                            reference += ": "
                    if publisher:
                        reference += f"{publisher}"
                reference += f", {year}."
                
            elif style_name.lower() == "chicago":
                # Chicago: Author. Title. Address: Publisher, Year.
                reference = f"{authors}. *{title}*. "
                if address:
                    reference += f"{address}: "
                if publisher:
                    reference += f"{publisher}, "
                reference += f"{year}."
                
            else:
                # Default/Plain: Author. Title. Publisher, Address, Year.
                reference = f"{authors}. *{title}*. "
                if publisher:
                    reference += f"{publisher}"
                    if address:
                        reference += f", {address}"
                reference += f", {year}."
        
        else:  # Other entry types
            # Generic format for misc entry types
            reference = f"{authors} ({year}). {title}."
        
        # Add DOI with proper Markdown link formatting if available
        if doi and "doi:" not in reference.lower() and "doi.org" not in reference.lower():
            reference += f" [doi:{doi}](https://doi.org/{doi})"
        
        # Format as a numbered reference
        markdown_reference = f"[{ref_id}]: {reference}"
        
        return citation_marker, markdown_reference

    def format_authors(self, entry, style_name):
        """Format authors according to the style."""
        if 'author' not in entry.persons and 'editor' not in entry.persons:
            return ""
        
        # Use editors if no authors are available
        if 'author' in entry.persons:
            authors = entry.persons['author']
        else:
            authors = entry.persons['editor']
            
        # IEEE, Vancouver: Use last name first with initials
        if style_name.lower() in ["ieee", "vancouver"]:
            if len(authors) == 1:
                return self.format_last_first(authors[0], True)
            elif len(authors) <= 7:
                names = [self.format_last_first(author, True) for author in authors[:-1]]
                names.append(f"and {self.format_last_first(authors[-1], True)}")
                return ", ".join(names)
            else:
                # More than 7 authors: show first 6 + et al.
                names = [self.format_last_first(author, True) for author in authors[:6]]
                names.append("et al.")
                return ", ".join(names)
        
        # Harvard, APA: Normal order with full first names, et al. for >3
        elif style_name.lower() in ["harvard1", "apa"]:
            if len(authors) > 7:
                # For APA with more than 7 authors: First 6 + ... + last author
                names = [self.format_name(author) for author in authors[:6]]
                names.append("...")
                names.append(self.format_name(authors[-1]))
                return ", ".join(names)
            elif len(authors) > 3:
                return f"{self.format_name(authors[0])} et al."
            elif len(authors) == 1:
                return self.format_name(authors[0])
            else:
                names = [self.format_name(author) for author in authors[:-1]]
                names.append(f"and {self.format_name(authors[-1])}")
                return ", ".join(names)
        
        # Nature: All authors in normal order
        elif style_name.lower() == "nature":
            if len(authors) == 1:
                return self.format_name(authors[0])
            else:
                names = [self.format_name(author) for author in authors[:-1]]
                names.append(f"& {self.format_name(authors[-1])}")
                return ", ".join(names)
        
        # Chicago: All authors in normal order
        elif style_name.lower() == "chicago":
            if len(authors) == 1:
                return self.format_name(authors[0])
            else:
                names = [self.format_name(author) for author in authors[:-1]]
                names.append(f"and {self.format_name(authors[-1])}")
                return ", ".join(names)
        
        # Default: Normal order
        else:
            if len(authors) == 1:
                return self.format_name(authors[0])
            else:
                names = [self.format_name(author) for author in authors[:-1]]
                names.append(f"and {self.format_name(authors[-1])}")
                return ", ".join(names)

    def format_name(self, person):
        """Format a person's name in normal order: First Middle Last"""
        first = " ".join(person.first_names)
        last = " ".join(person.last_names)
        return f"{first} {last}"
        
    def format_last_first(self, person, initials=False):
        """Format a person's name as Last, First or Last, F."""
        if initials:
            first = " ".join([name[0] + "." for name in person.first_names])
        else:
            first = " ".join(person.first_names)
        
        last = " ".join(person.last_names)
        
        if first:
            return f"{last}, {first}"
        else:
            return last

    def process_web_reference(self, web_data, ref_id):
        """
        Convert a web reference to a formatted citation according to style.
        
        Args:
            web_data: Dictionary with web reference data (title, url, etc.)
            ref_id: Reference ID for citation
            
        Returns:
            tuple: (citation_marker, reference_entry)
        """
        citation_marker = f"[{ref_id}]"
        
        # Extract web data
        title = web_data.get("title", "Web Page")
        url = web_data.get("url", "")
        date = web_data.get("date", "")
        
        # If no date is provided, use current date
        if not date:
            from datetime import datetime
            date = datetime.now().strftime("%B %d, %Y")
        
        # Format according to APA style for websites
        markdown_reference = f"[{ref_id}] {title}. "
        
        # Add date if available
        if date:
            markdown_reference += f"({date}). "
        
        # Add URL
        markdown_reference += f"Retrieved from [{url}]({url})"
        
        return citation_marker, markdown_reference

    def process_file_reference(self, filepath, ref_id, description=None):
        """
        Convert a filepath to a markdown reference with clickable link.
        
        Args:
            filepath: Path to the file
            ref_id: Reference ID for citation
            description: Optional description for the file
            
        Returns:
            tuple: (citation_marker, reference_entry)
        """
        citation_marker = f"[{ref_id}]"
        
        # Create file basename for display
        filename = os.path.basename(filepath)
        
        # Create clickable URL in the specific format:
        # https://filecloud.vicebio.com/ui/core/index.html?filter=FILENAME#expl-tabl.%2FSHARED%2Fvicebio_shares%2FPATH
        
        # Escape spaces in filename with + for the first part
        encoded_filename = filename.replace(' ', '+')
        
        # Encode path for the second part (after #expl-tabl.)
        # Extract directory path without filename
        directory_path = os.path.dirname(filepath)
        # Ensure path ends with '/'
        if directory_path and not directory_path.endswith('/'):
            directory_path += '/'
        
        encoded_path = f"/SHARED/vicebio_shares/{directory_path}"
        encoded_path = encoded_path.replace(' ', '%20')
        
        # Construct the full URL
        file_url = f"https://filecloud.vicebio.com/ui/core/index.html?filter={encoded_filename}#expl-tabl.{encoded_path}"
        
        # Create the reference with description if provided
        if description:
            markdown_reference = f"[{ref_id}]: **{description}**: [{filename}]({file_url})"
        else:
            markdown_reference = f"[{ref_id}]: [{filename}]({file_url})"
        
        return citation_marker, markdown_reference

    def generate_references_section(self, references, style="apa"):
        """
        Generate a complete references section in Markdown from a list of reference objects.
        
        Args:
            references: List of reference objects (dictionaries with required fields)
            style: Citation style to use (e.g., 'apa', 'ieee', 'nature', etc.)
            
        Returns:
            tuple: (markdown_output, citation_map)
        """
        title = self.style_titles.get(style.lower(), "References")
        markdown_output = f"## {title}\n\n"
        citation_map = {}
        
        # Format each reference
        for ref in references:
            ref_id = ref["id"]
            ref_type = ref["type"]
            
            if ref_type == "bibtex":
                citation, reference = self.format_bibtex_reference(ref["content"], ref_id, style)
            elif ref_type == "file" or ref_type == "document":
                description = ref.get("description", None)
                citation, reference = self.process_file_reference(ref["path"], ref_id, description)
            elif ref_type == "web":
                citation, reference = self.process_web_reference(ref, ref_id)
            else:
                # Simple text reference
                citation_marker = f"[{ref_id}]"
                markdown_reference = f"[{ref_id}]: {ref.get('content', 'Reference')}"
                citation, reference = citation_marker, markdown_reference
                
            markdown_output += reference + "\n\n"
            citation_map[ref_id] = citation
        
        return markdown_output.strip(), citation_map

    def list_available_styles(self):
        """
        List all available citation styles
        
        Returns:
            list: Names of available styles
        """
        return ["apa", "ieee", "chicago", "harvard1", "nature", "vancouver", "plain"]