app.py

import os
import time
import pdfplumber
import docx
import nltk
import gradio as gr
from langchain_huggingface import HuggingFaceEmbeddings
from langchain_community.embeddings import CohereEmbeddings
from langchain_openai import OpenAIEmbeddings
from langchain_community.vectorstores import FAISS, Chroma
from langchain_text_splitters import RecursiveCharacterTextSplitter, TokenTextSplitter
from typing import List, Dict, Any
import pandas as pd
import numpy as np
import re
from nltk.corpus import stopwords
from nltk.tokenize import word_tokenize
from nltk.stem import SnowballStemmer
import jellyfish
from gensim.models import Word2Vec
from gensim.models.fasttext import FastText
from collections import Counter
from tokenizers import Tokenizer, models, trainers
from tokenizers.models import WordLevel
from tokenizers.trainers import WordLevelTrainer
from tokenizers.pre_tokenizers import Whitespace
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.manifold import TSNE
from sklearn.metrics import silhouette_score
from scipy.stats import spearmanr
from functools import lru_cache

# NLTK Resource Download
def download_nltk_resources():
    resources = ['punkt', 'stopwords', 'snowball_data']
    for resource in resources:
        try:
            nltk.download(resource, quiet=True)
        except Exception as e:
            print(f"Failed to download {resource}: {str(e)}")

download_nltk_resources()

FILES_DIR = './files'

# Model Management
class ModelManager:
    def __init__(self):
        self.models = {
            'HuggingFace': {
                'e5-base-de': "danielheinz/e5-base-sts-en-de",
                'paraphrase-miniLM': "paraphrase-multilingual-MiniLM-L12-v2",
                'paraphrase-mpnet': "paraphrase-multilingual-mpnet-base-v2",
                'gte-large': "gte-large",
                'gbert-base': "gbert-base"
            },
            'OpenAI': {
                'text-embedding-ada-002': "text-embedding-ada-002"
            },
            'Cohere': {
                'embed-multilingual-v2.0': "embed-multilingual-v2.0"
            }
        }

    def add_model(self, provider, name, model_path):
        if provider not in self.models:
            self.models[provider] = {}
        self.models[provider][name] = model_path

    def remove_model(self, provider, name):
        if provider in self.models and name in self.models[provider]:
            del self.models[provider][name]

    def get_model(self, provider, name):
        return self.models.get(provider, {}).get(name)

    def list_models(self):
        return {provider: list(models.keys()) for provider, models in self.models.items()}

model_manager = ModelManager()

# File Handling
class FileHandler:
    @staticmethod
    def extract_text(file_path):
        ext = os.path.splitext(file_path)[-1].lower()
        if ext == '.pdf':
            return FileHandler._extract_from_pdf(file_path)
        elif ext == '.docx':
            return FileHandler._extract_from_docx(file_path)
        elif ext == '.txt':
            return FileHandler._extract_from_txt(file_path)
        else:
            raise ValueError(f"Unsupported file type: {ext}")

    @staticmethod
    def _extract_from_pdf(file_path):
        with pdfplumber.open(file_path) as pdf:
            return ' '.join([page.extract_text() for page in pdf.pages])

    @staticmethod
    def _extract_from_docx(file_path):
        doc = docx.Document(file_path)
        return ' '.join([para.text for para in doc.paragraphs])

    @staticmethod
    def _extract_from_txt(file_path):
        with open(file_path, 'r', encoding='utf-8') as f:
            return f.read()

# Text Processing
def simple_tokenize(text):
    return text.split()

def preprocess_text(text, lang='german'):
    text = text.lower()
    text = re.sub(r'[^a-zA-Z\s]', '', text)
    
    try:
        tokens = word_tokenize(text, language=lang)
    except LookupError:
        print(f"Warning: NLTK punkt tokenizer for {lang} not found. Using simple tokenization.")
        tokens = simple_tokenize(text)
    
    try:
        stop_words = set(stopwords.words(lang))
    except LookupError:
        print(f"Warning: Stopwords for {lang} not found. Skipping stopword removal.")
        stop_words = set()
    tokens = [token for token in tokens if token not in stop_words]
    
    try:
        stemmer = SnowballStemmer(lang)
        tokens = [stemmer.stem(token) for token in tokens]
    except ValueError:
        print(f"Warning: SnowballStemmer for {lang} not available. Skipping stemming.")
    
    return ' '.join(tokens)

def phonetic_match(text, query, method='levenshtein_distance'):
    if method == 'levenshtein_distance':
        text_phonetic = jellyfish.soundex(text)
        #query_phonetic = jellyfish.cologne_phonetic(query)
        query_phonetic = jellyfish.soundex(query)
        return jellyfish.levenshtein_distance(text_phonetic, query_phonetic)
    return 0

def create_custom_embedding(texts, model_type='word2vec', vector_size=100, window=5, min_count=1):
    # Tokenize the texts
    tokenized_texts = [text.split() for text in texts]
    
    if model_type == 'word2vec':
        model = Word2Vec(sentences=tokenized_texts, vector_size=vector_size, window=window, min_count=min_count, workers=4)
    elif model_type == 'fasttext':
        model = FastText(sentences=tokenized_texts, vector_size=vector_size, window=window, min_count=min_count, workers=4)
    else:
        raise ValueError("Unsupported model type")
    
    return model

class CustomEmbeddings(HuggingFaceEmbeddings):
    def __init__(self, model_path):
        self.model = Word2Vec.load(model_path)  # or FastText.load() for FastText models
    
    def embed_documents(self, texts):
        return [self.model.wv[text.split()] for text in texts]
    
    def embed_query(self, text):
        return self.model.wv[text.split()]


# Custom Tokenizer
def create_custom_tokenizer(file_path):
    with open(file_path, 'r', encoding='utf-8') as f:
        text = f.read()

    tokenizer = Tokenizer(WordLevel(unk_token="[UNK]"))
    tokenizer.pre_tokenizer = Whitespace()

    trainer = WordLevelTrainer(special_tokens=["[UNK]", "[CLS]", "[SEP]", "[PAD]", "[MASK]"])
    tokenizer.train_from_iterator([text], trainer)

    return tokenizer

def custom_tokenize(text, tokenizer):
    return tokenizer.encode(text).tokens

# Embedding and Vector Store
@lru_cache(maxsize=None)
def get_embedding_model(model_type, model_name):
    model_path = model_manager.get_model(model_type, model_name)
    if model_type == 'HuggingFace':
        return HuggingFaceEmbeddings(model_name=model_path)
    elif model_type == 'OpenAI':
        return OpenAIEmbeddings(model=model_path)
    elif model_type == 'Cohere':
        return CohereEmbeddings(model=model_path)
    else:
        raise ValueError(f"Unsupported model type: {model_type}")

def get_text_splitter(split_strategy, chunk_size, overlap_size, custom_separators=None):
    if split_strategy == 'token':
        return TokenTextSplitter(chunk_size=chunk_size, chunk_overlap=overlap_size)
    elif split_strategy == 'recursive':
        return RecursiveCharacterTextSplitter(
            chunk_size=chunk_size,
            chunk_overlap=overlap_size,
            separators=custom_separators or ["\n\n", "\n", " ", ""]
        )
    else:
        raise ValueError(f"Unsupported split strategy: {split_strategy}")

def get_vector_store(vector_store_type, chunks, embedding_model):
    # Convert chunks to a tuple to make it hashable
    chunks_tuple = tuple(chunks)
    
    # Use a helper function for the actual vector store creation
    return _create_vector_store(vector_store_type, chunks_tuple, embedding_model)


def _create_vector_store(vector_store_type, chunks_tuple, embedding_model):
    # Convert the tuple back to a list for use with the vector store
    chunks = list(chunks_tuple)
    
    if vector_store_type == 'FAISS':
        return FAISS.from_texts(chunks, embedding_model)
    elif vector_store_type == 'Chroma':
        return Chroma.from_texts(chunks, embedding_model)
    else:
        raise ValueError(f"Unsupported vector store type: {vector_store_type}")

        
def get_retriever(vector_store, search_type, search_kwargs):
    if search_type == 'similarity':
        return vector_store.as_retriever(search_type="similarity", search_kwargs=search_kwargs)
    elif search_type == 'mmr':
        return vector_store.as_retriever(search_type="mmr", search_kwargs=search_kwargs)
    elif search_type == 'custom':
        # Implement custom retriever logic here
        pass
    else:
        raise ValueError(f"Unsupported search type: {search_type}")

# Main Processing Functions
def process_files(file_path, model_type, model_name, split_strategy, chunk_size, overlap_size, custom_separators, lang='german', custom_tokenizer_file=None):
    if file_path:
        text = FileHandler.extract_text(file_path)
    else:
        text = ""
        for file in os.listdir(FILES_DIR):
            file_path = os.path.join(FILES_DIR, file)
            text += FileHandler.extract_text(file_path)
    
    if custom_tokenizer_file:
        tokenizer = create_custom_tokenizer(custom_tokenizer_file)
        text = ' '.join(custom_tokenize(text, tokenizer))
    else:
        text = preprocess_text(text, lang)

    text_splitter = get_text_splitter(split_strategy, chunk_size, overlap_size, custom_separators)
    chunks = text_splitter.split_text(text)

    embedding_model = get_embedding_model(model_type, model_name)

    return chunks, embedding_model, len(text.split())

def search_embeddings(chunks, embedding_model, vector_store_type, search_type, query, top_k, lang='german', phonetic_weight=0.3):
    preprocessed_query = preprocess_text(query, lang)
    
    vector_store = get_vector_store(vector_store_type, chunks, embedding_model)
    retriever = get_retriever(vector_store, search_type, {"k": top_k})

    start_time = time.time()
    results = retriever.invoke(preprocessed_query)

    def score_result(doc):
        similarity_score = vector_store.similarity_search_with_score(doc.page_content, k=1)[0][1]
        phonetic_score = phonetic_match(doc.page_content, query)
        return (1 - phonetic_weight) * similarity_score + phonetic_weight * phonetic_score

    results = sorted(results, key=score_result, reverse=True)
    end_time = time.time()

    # Check if embeddings are available
    embeddings = []
    for doc in results:
        if hasattr(doc, 'embedding'):
            embeddings.append(doc.embedding)  # Use the embedding if it exists
        else:
            embeddings.append(None)  # Append None if embedding doesn't exist

    # Create a DataFrame with the results and embeddings
    results_df = pd.DataFrame({
        'content': [doc.page_content for doc in results],
        'embedding': embeddings
    })

    return results_df, end_time - start_time, vector_store, results

# Evaluation Metrics
def calculate_statistics(results, search_time, vector_store, num_tokens, embedding_model, query, top_k):
    stats = {
        "num_results": len(results),
 #       "avg_content_length": sum(len(doc.page_content) for doc in results) / len(results) if results else 0,
        "avg_content_length": np.mean([len(doc.page_content) for doc in results]) if results else 0,

        #"avg_content_length": np.mean([len(doc.page_content) for doc in results]) if not results.empty else 0,
        "search_time": search_time,
        "vector_store_size": vector_store._index.ntotal if hasattr(vector_store, '_index') else "N/A",
        "num_documents": len(vector_store.docstore._dict),
        "num_tokens": num_tokens,
        "embedding_vocab_size": embedding_model.client.get_vocab_size() if hasattr(embedding_model, 'client') and hasattr(embedding_model.client, 'get_vocab_size') else "N/A",
        "embedding_dimension": len(embedding_model.embed_query(query)),
        "top_k": top_k,
    }
    
    if len(results) > 1000:
        embeddings = [embedding_model.embed_query(doc.page_content) for doc in results]
        pairwise_similarities = np.inner(embeddings, embeddings)
        stats["result_diversity"] = 1 - np.mean(pairwise_similarities[np.triu_indices(len(embeddings), k=1)])
        
        # Silhouette Score
        if len(embeddings) > 2:
            print('-----')
            #stats["silhouette_score"] = "N/A"
            stats["silhouette_score"] = silhouette_score(embeddings, range(len(embeddings)))
        else:
            stats["silhouette_score"] = "N/A"
    else:
        stats["result_diversity"] = "N/A"
        stats["silhouette_score"] = "N/A"
    
    query_embedding = embedding_model.embed_query(query)
    result_embeddings = [embedding_model.embed_query(doc.page_content) for doc in results]
    similarities = [np.inner(query_embedding, emb) for emb in result_embeddings]
    rank_correlation, _ = spearmanr(similarities, range(len(similarities)))
    stats["rank_correlation"] = rank_correlation
    
    return stats

# Visualization
def visualize_results(results_df, stats_df):
    fig, axs = plt.subplots(2, 2, figsize=(20, 20))
    
    sns.barplot(x='model', y='search_time', data=stats_df, ax=axs[0, 0])
    axs[0, 0].set_title('Search Time by Model')
    axs[0, 0].set_xticklabels(axs[0, 0].get_xticklabels(), rotation=45, ha='right')
    
    sns.scatterplot(x='result_diversity', y='rank_correlation', hue='model', data=stats_df, ax=axs[0, 1])
    axs[0, 1].set_title('Result Diversity vs. Rank Correlation')
    
    sns.boxplot(x='model', y='avg_content_length', data=stats_df, ax=axs[1, 0])
    axs[1, 0].set_title('Distribution of Result Content Lengths')
    axs[1, 0].set_xticklabels(axs[1, 0].get_xticklabels(), rotation=45, ha='right')
    
    embeddings = np.array([embedding for embedding in results_df['embedding'] if isinstance(embedding, np.ndarray)])
    if len(embeddings) > 1:
        tsne = TSNE(n_components=2, random_state=42)
        embeddings_2d = tsne.fit_transform(embeddings)
        
        sns.scatterplot(x=embeddings_2d[:, 0], y=embeddings_2d[:, 1], hue=results_df['model'][:len(embeddings)], ax=axs[1, 1])
        axs[1, 1].set_title('t-SNE Visualization of Result Embeddings')
    else:
        axs[1, 1].text(0.5, 0.5, "Not enough data for t-SNE visualization", ha='center', va='center')
    
    plt.tight_layout()
    return fig

def optimize_vocabulary(texts, vocab_size=10000, min_frequency=2):
    tokenizer = Tokenizer(models.BPE(unk_token="[UNK]"))

    # Count word frequencies
    word_freq = Counter(word for text in texts for word in text.split())
    
    # Remove rare words
    optimized_texts = [
        ' '.join(word for word in text.split() if word_freq[word] >= min_frequency)
        for text in texts
    ]
    
    # Train BPE tokenizer
#    tokenizer = Tokenizer(BPE(unk_token="[UNK]"))
    trainer = trainers.BpeTrainer(vocab_size=vocab_size, special_tokens=["[UNK]", "[CLS]", "[SEP]", "[PAD]", "[MASK]"])
    tokenizer.train_from_iterator(optimized_texts, trainer)
    
    return tokenizer, optimized_texts

# Main Comparison Function
def compare_embeddings(file, query, model_types, model_names, split_strategy, chunk_size, overlap_size, custom_separators, vector_store_type, search_type, top_k, lang='german', use_custom_embedding=False, optimize_vocab=False, phonetic_weight=0.3, custom_tokenizer_file=None):
    all_results = []
    all_stats = []
    settings = {
        "split_strategy": split_strategy,
        "chunk_size": chunk_size,
        "overlap_size": overlap_size,
        "custom_separators": custom_separators,
        "vector_store_type": vector_store_type,
        "search_type": search_type,
        "top_k": top_k,
        "lang": lang,
        "use_custom_embedding": use_custom_embedding,
        "optimize_vocab": optimize_vocab,
        "phonetic_weight": phonetic_weight
    }

    for model_type, model_name in zip(model_types, model_names):
        # Process the file and generate chunks & embeddings
        chunks, embedding_model, num_tokens = process_files(
            file.name if file else None,
            model_type,
            model_name,
            split_strategy,
            chunk_size,
            overlap_size,
            custom_separators.split(',') if custom_separators else None,
            lang,
            custom_tokenizer_file
        )

        # Custom embedding handling
        if use_custom_embedding:
            custom_model = create_custom_embedding(chunks) #add custom model by name, must com from gradio FE
            embedding_model = CustomEmbeddings(custom_model)

        # Optimizing vocabulary if required
        if optimize_vocab:
            tokenizer, optimized_chunks = optimize_vocabulary(chunks)
            chunks = optimized_chunks

        # Searching embeddings
        results, search_time, vector_store, results_raw = search_embeddings(
            chunks,
            embedding_model,
            vector_store_type,
            search_type,
            query,
            top_k,
            lang,
            phonetic_weight
        )

        # Storing embeddings into the results for future use
        for doc in results_raw:
            print(doc)  # or print(dir(doc)) to see available attributes

        #embedding = doc.metadata.get('embedding', None)  # Use .get() to avoid KeyError

        result_embeddings = [doc.metadata.get('embedding', None) for doc in results_raw]  # Adjust this based on the actual attribute names
#        result_embeddings = [doc['embedding'] for doc in results_raw]  # Assuming each result has an embedding

        stats = calculate_statistics(results_raw, search_time, vector_store, num_tokens, embedding_model, query, top_k)
        stats["model"] = f"{model_type} - {model_name}"
        stats.update(settings)

        # Formatting results and attaching embeddings
        formatted_results = format_results(results_raw, stats)
        for i, result in enumerate(formatted_results):
            result['embedding'] = result_embeddings[i]  # Add the embedding to each result

        all_results.extend(formatted_results)
        all_stats.append(stats)

    # Create DataFrames with embeddings now included
    results_df = pd.DataFrame(all_results)
    stats_df = pd.DataFrame(all_stats)

    # Visualization of the results
    fig = visualize_results(results_df, stats_df)

    return results_df, stats_df, fig

def format_results(results, stats):
    formatted_results = []
    for doc in results:
        result = {
            "Model": stats["model"],
            "Content": doc.page_content,
            "Embedding": doc.embedding if hasattr(doc, 'embedding') else None,
            **doc.metadata,
            **{k: v for k, v in stats.items() if k not in ["model"]}
        }
        formatted_results.append(result)
    return formatted_results

# Gradio Interface
def launch_interface(share=True):
    iface = gr.Interface(
        fn=compare_embeddings,
        inputs=[
            gr.File(label="Upload File (Optional)"),
            gr.Textbox(label="Search Query"),
            gr.CheckboxGroup(choices=list(model_manager.list_models().keys()) + ["Custom"], label="Embedding Model Types"),
            gr.CheckboxGroup(choices=[model for models in model_manager.list_models().values() for model in models] + ["custom_model"], label="Embedding Models"),
            gr.Radio(choices=["token", "recursive"], label="Split Strategy", value="recursive"),
            gr.Slider(100, 1000, step=100, value=500, label="Chunk Size"),
            gr.Slider(0, 100, step=10, value=50, label="Overlap Size"),
            gr.Textbox(label="Custom Split Separators (comma-separated, optional)"),
            gr.Radio(choices=["FAISS", "Chroma"], label="Vector Store Type", value="FAISS"),
            gr.Radio(choices=["similarity", "mmr", "custom"], label="Search Type", value="similarity"),
            gr.Slider(1, 10, step=1, value=5, label="Top K"),
            gr.Dropdown(choices=["german", "english", "french"], label="Language", value="german"),
            gr.Checkbox(label="Use Custom Embedding", value=False),
            gr.Checkbox(label="Optimize Vocabulary", value=False),
            gr.Slider(0, 1, step=0.1, value=0.3, label="Phonetic Matching Weight"),
            gr.File(label="Custom Tokenizer File (Optional)")
        ],
        outputs=[
            gr.Dataframe(label="Results", interactive=False),
            gr.Dataframe(label="Statistics", interactive=False),
            gr.Plot(label="Visualizations")
        ],
        title="Advanced Embedding Comparison Tool",
        description="Compare different embedding models and retrieval strategies with advanced preprocessing and phonetic matching"
    )

    tutorial_md = """
    # Advanced Embedding Comparison Tool Tutorial

    This tool allows you to compare different embedding models and retrieval strategies for document search and similarity matching.

    ## How to use:

    1. Upload a file (optional) or use the default files in the system.
    2. Enter a search query.
    3. Select one or more embedding model types and specific models.
    4. Choose a text splitting strategy and set chunk size and overlap.
    5. Select a vector store type and search type.
    6. Set the number of top results to retrieve.
    7. Choose the language of your documents.
    8. Optionally, use custom embeddings, optimize vocabulary, or adjust phonetic matching weight.
    9. If you have a custom tokenizer, upload the file.

    The tool will process your query and display results, statistics, and visualizations to help you compare the performance of different models and strategies.
    """

    iface = gr.TabbedInterface(
        [iface, gr.Markdown(tutorial_md)],
        ["Embedding Comparison", "Tutorial"]
    )

    iface.launch(share=share)

if __name__ == "__main__":
    launch_interface()