RAG_utils.py

import os
import re
import json
import torch

import openai
import logging
import asyncio
import aiohttp
import pandas as pd
import numpy as np
import evaluate
import qdrant_client
from pypdf import PdfReader
from pydantic import BaseModel, Field
from typing import Any, List, Tuple, Set, Dict, Optional, Union
from sklearn.metrics.pairwise import cosine_similarity

from unstructured.partition.pdf import partition_pdf

import llama_index
from llama_index import PromptTemplate
from llama_index.retrievers import VectorIndexRetriever, BaseRetriever, BM25Retriever
from llama_index.query_engine import RetrieverQueryEngine
from llama_index import get_response_synthesizer
from llama_index.schema import NodeWithScore
from llama_index.query_engine import RetrieverQueryEngine
from llama_index import VectorStoreIndex, ServiceContext
from llama_index.embeddings import OpenAIEmbedding
from llama_index.llms import HuggingFaceLLM
import requests
from llama_index.llms import (
    CustomLLM,
    CompletionResponse,
    CompletionResponseGen,
    LLMMetadata,
)
from llama_index.query_engine import RetrieverQueryEngine
from llama_index.llms.base import llm_completion_callback
from llama_index.vector_stores.qdrant import QdrantVectorStore
from llama_index.storage.storage_context import StorageContext
from llama_index.postprocessor import SentenceTransformerRerank, LLMRerank

from tempfile import NamedTemporaryFile
# Configure basic logging
logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')

# Create a logger object
logger = logging.getLogger(__name__)

class ConfigManager:
    """
    A class to manage loading and accessing configuration settings.

    Attributes:
        config (dict): Dictionary to hold configuration settings.

    Methods:
        load_config(config_path: str): Loads the configuration from a given JSON file.
        get_config_value(key: str): Retrieves a specific configuration value.
    """

    def __init__(self):
        self.configs = {}
        
    def load_config(self, config_name: str, config_path: str) -> None:
        """
        Loads configuration settings from a specified JSON file into a named configuration.

        Args:
            config_name (str): The name to assign to this set of configurations.
            config_path (str): The path to the configuration file.

        Raises:
            FileNotFoundError: If the config file is not found.
            json.JSONDecodeError: If there is an error parsing the config file.
        """
        try:
            with open(config_path, 'r') as f:
                self.configs[config_name] = json.load(f)
        except FileNotFoundError:
            logging.error(f"Config file not found at {config_path}")
            raise
        except json.JSONDecodeError as e:
            logging.error(f"Error decoding config file: {e}")
            raise


    def get_config_value(self, config_name: str, key: str) -> str:
        """
        Retrieves a specific configuration value.

        Args:
            key (str): The key for the configuration setting.

        Returns:
            str: The value of the configuration setting.

        Raises:
            ValueError: If the key is not found or is set to a placeholder value.
        """
        value = self.configs.get(config_name, {}).get(key)
        if value is None or value == "ENTER_YOUR_TOKEN_HERE":
            raise ValueError(f"Please set your '{key}' in the config.json file.")
        return value

class base_utils:
    """
    A utility class providing miscellaneous static methods for processing and analyzing text data,
    particularly from PDF documents and filenames. This class also includes methods for file operations.

    This class encapsulates the functionality of extracting key information from text, such as scores,
    reasoning, and IDs, locating specific data within a DataFrame based on an ID extracted from a filename,
    and reading content from files.

    Attributes:
        None (This class contains only static methods and does not maintain any state)

    Methods:
        extract_score_reasoning(text: str) -> Dict[str, Optional[str]]:
            Extracts a score and reasoning from a given text using regular expressions.

        extract_id_from_filename(filename: str) -> Optional[int]:
            Extracts an ID from a given filename based on a specified pattern.

        find_row_for_pdf(pdf_filename: str, dataframe: pd.DataFrame) -> Union[pd.Series, str]:
            Searches for a row in a DataFrame that matches an ID extracted from a PDF filename.

        read_from_file(file_path: str) -> str:
            Reads the content of a file and returns it as a string.
    """
    
    @staticmethod
    def read_from_file(file_path: str) -> str:
        """
        Reads the content of a file and returns it as a string.

        Args:
            file_path (str): The path to the file to be read.

        Returns:
            str: The content of the file.
        """
        with open(file_path, 'r') as prompt_file:
            prompt = prompt_file.read()
        return prompt
        
    @staticmethod
    def extract_id_from_filename(filename: str) -> Optional[int]:
        """
        Extracts an ID from a filename, assuming a specific format ('Id_{I}.pdf', where {I} is the ID).

        Args:
            filename (str): The filename from which to extract the ID.

        Returns:
            int: The extracted ID as an integer, or None if the pattern is not found.
        """
        # Assuming the file name is in the format 'Id_{I}.pdf', where {I} is the ID
        match = re.search(r'Id_(\d+).pdf', filename)
        if match:
            return int(match.group(1))  # Convert to integer if ID is numeric
        else:
            return None
    
    @staticmethod
    def extract_score_reasoning(text: str) -> Dict[str, Optional[str]]:
        """
        Extracts score and reasoning from a given text using regular expressions.

        Args:
            text (str): The text from which to extract the score and reasoning.

        Returns:
            dict: A dictionary containing 'score' and 'reasoning', extracted from the text.
        """
        # Define regular expression patterns for score and reasoning
        score_pattern = r"Score: (\d+)"
        reasoning_pattern = r"Reasoning: (.+)"
        
        # Extract data using regular expressions
        score_match = re.search(score_pattern, text)
        reasoning_match = re.search(reasoning_pattern, text, re.DOTALL)  # re.DOTALL allows '.' to match newlines
        
        # Extract and return the results
        extracted_data = {
            "score": score_match.group(1) if score_match else None,
            "reasoning": reasoning_match.group(1).strip() if reasoning_match else None
        }
        
        return extracted_data
            
            
    @staticmethod
    def find_row_for_pdf(pdf_filename: str, dataframe: pd.DataFrame) -> Union[pd.Series, str]:
        """
        Finds the row in a dataframe corresponding to the ID extracted from a given PDF filename.

        Args:
            pdf_filename (str): The filename of the PDF.
            dataframe (pandas.DataFrame): The dataframe in which to find the corresponding row.

        Returns:
            pandas.Series or str: The matched row from the dataframe or a message indicating
                                  that no matching row or invalid filename was found.
        """
        pdf_id = Utility.extract_id_from_filename(pdf_filename)
        if pdf_id is not None:
            # Assuming the first column contains the ID
            matched_row = dataframe[dataframe.iloc[:, 0] == pdf_id]
            if not matched_row.empty:
                return matched_row
            else:
                return "No matching row found."
        else:
            return "Invalid file name."
            
            
class PDFProcessor_Unstructured:
    """
    A class to process PDF files, providing functionalities for extracting, categorizing,
    and merging elements from a PDF file.

    This class is designed to handle unstructured PDF documents, particularly useful for
    tasks involving text extraction, categorization, and data processing within PDFs.

    Attributes:
        file_path (str): The full path to the PDF file.
        folder_path (str): The directory path where the PDF file is located.
        file_name (str): The name of the PDF file.
        texts (List[str]): A list to store extracted text chunks.
        tables (List[str]): A list to store extracted tables.
        

    Methods:
        extract_pdf_elements() -> List:
            Extracts images, tables, and text chunks from a PDF file.

        categorize_elements(raw_pdf_elements: List) -> None:
            Categorizes extracted elements from a PDF into tables and texts.

        merge_chunks() -> List[str]:
            Merges text chunks based on punctuation and character case criteria.

        should_skip_chunk(chunk: str) -> bool:
            Determines if a chunk should be skipped based on its content.

        should_merge_with_next(current_chunk: str, next_chunk: str) -> bool:
            Determines if the current chunk should be merged with the next one.

        process_pdf() -> Tuple[List[str], List[str]]:
            Processes the PDF by extracting, categorizing, and merging elements.

        process_pdf_file(uploaded_file) -> Tuple[List[str], List[str]]:
            Processes an uploaded PDF file to extract and categorize text and tables.
    """

    def __init__(self, config: Dict[str, any]):
        self.file_path = None
        self.folder_path = None
        self.file_name = None
        self.texts = []
        self.tables = []
        self.config = config if config is not None else self.default_config()
        logger.info(f"Initialized PdfProcessor_Unstructured for file: {self.file_name}")
        
    @staticmethod
    def default_config() -> Dict[str, any]:
        """
        Returns the default configuration for PDF processing.

        Returns:
            Dict[str, any]: Default configuration options.
        """
        return {
            "extract_images": False,
            "infer_table_structure": True,
            "chunking_strategy": "by_title",
            "max_characters": 10000,
            "combine_text_under_n_chars": 100,
            "strategy": "fast",
            "model_name": "yolox"
        }


    def extract_pdf_elements(self) -> List:
        """
        Extracts images, tables, and text chunks from a PDF file.

        Returns:
            List: A list of extracted elements from the PDF.
        """
        logger.info("Starting extraction of PDF elements.")
        try:
            extracted_elements = partition_pdf(
                filename=self.file_path,
                extract_images_in_pdf=False,
                infer_table_structure=True,
                chunking_strategy="by_title",
                strategy = "fast",
                max_characters=10000,
                combine_text_under_n_chars=100,
                image_output_dir_path=self.folder_path,
            )
            logger.info("Extraction of PDF elements completed successfully.")
            return extracted_elements
        except Exception as e:
            logger.error(f"Error extracting PDF elements: {e}", exc_info=True)
            raise

    def categorize_elements(self, raw_pdf_elements: List) -> None:
        """
        Categorizes extracted elements from a PDF into tables and texts.

        Args:
            raw_pdf_elements (List): A list of elements extracted from the PDF.
        """
        logger.debug("Starting categorization of PDF elements.")
        for element in raw_pdf_elements:
            element_type = str(type(element))
            if "unstructured.documents.elements.Table" in element_type:
                self.tables.append(str(element))
            elif "unstructured.documents.elements.CompositeElement" in element_type:
                self.texts.append(str(element))
                
        logger.debug("Categorization of PDF elements completed.")

    def merge_chunks(self) -> List[str]:
        """
        Merges text chunks based on punctuation and character case criteria.

        Returns:
            List[str]: A list of merged text chunks.
        """
        logger.debug("Starting merging of text chunks.")
        
        merged_chunks = []
        skip_next = False

        for i, current_chunk in enumerate(self.texts[:-1]):
            next_chunk = self.texts[i + 1]

            if self.should_skip_chunk(current_chunk):
                continue

            if self.should_merge_with_next(current_chunk, next_chunk):
                merged_chunks.append(current_chunk + " " + next_chunk)
                skip_next = True
            else:
                merged_chunks.append(current_chunk)

        if not skip_next:
            merged_chunks.append(self.texts[-1])
        
        logger.debug("Merging of text chunks completed.")

        return merged_chunks

    @staticmethod
    def should_skip_chunk(chunk: str) -> bool:
        """
        Determines if a chunk should be skipped based on its content.

        Args:
            chunk (str): The text chunk to be evaluated.

        Returns:
            bool: True if the chunk should be skipped, False otherwise.
        """
        return (chunk.lower().startswith(("figure", "fig", "table")) or
                not chunk[0].isalnum() or
                re.match(r'^\d+\.', chunk))

    @staticmethod
    def should_merge_with_next(current_chunk: str, next_chunk: str) -> bool:
        """
        Determines if the current chunk should be merged with the next one.

        Args:
            current_chunk (str): The current text chunk.
            next_chunk (str): The next text chunk.

        Returns:
            bool: True if the chunks should be merged, False otherwise.
        """
        return (current_chunk.endswith(",") or
                (current_chunk[-1].islower() and next_chunk[0].islower()))

    def extract_title_from_pdf(self, uploaded_file):
        """
        Extracts the title from a PDF file's metadata.

        This function reads the metadata of a PDF file using PyPDF2 and attempts to
        extract the title. If the title is present in the metadata, it is returned.
        Otherwise, a default message indicating that the title was not found is returned.

        Parameters:
        uploaded_file (file): A file object or a path to the PDF file from which
                          to extract the title. The file must be opened in binary mode.

        Returns:
        str: The title of the PDF file as a string. If no title is found, returns
             'Title not found'.
        """
        # Initialize PDF reader
        pdf_reader = PdfFileReader(uploaded_file)
        
        # Extract document information
        meta = pdf_reader.getDocumentInfo()
        
        # Retrieve title from document information
        title = meta.title if meta and meta.title else 'Title not found'
        return title

    def process_pdf(self) -> Tuple[List[str], List[str]]:
        """
        Processes the PDF by extracting, categorizing, and merging elements.

        Returns:
            Tuple[List[str], List[str]]: A tuple of merged text chunks and tables.
        """
        logger.info("Starting processing of the PDF.")
        try:
            raw_pdf_elements = self.extract_pdf_elements()
            self.categorize_elements(raw_pdf_elements)
            merged_chunks = self.merge_chunks()
            return merged_chunks, self.tables
        except Exception as e:
            logger.error(f"Error processing PDF: {e}", exc_info=True)
            raise
            
    def process_pdf_file(self, uploaded_file):
        """
        Process an uploaded PDF file.

        If a new file is uploaded, the previously stored file is deleted.
        The method updates the file path, processes the PDF, and returns the results.
        
        Parameters:
        uploaded_file: The new PDF file uploaded for processing.

        Returns:
        The results of processing the PDF file.
        """
        # Delete the previous file if it exists
        if self.file_path and os.path.exists(self.file_path):
            try:
                os.remove(self.file_path)
                logging.debug(f"Previous file {self.file_path} deleted.")
            except Exception as e:
                logging.warning(f"Error deleting previous file: {e}", exc_info=True)

        # Process the new file
        self.file_path = str(uploaded_file)
        self.folder_path = os.path.dirname(self.file_path)
        logging.info(f"Starting to process the PDF file: {self.file_path}")

        try:
            logging.debug(f"Processing PDF at {self.file_path}")
            results = self.process_pdf()
            title = extract_title_from_pdf(self.file_path)
            logging.info("PDF processing completed successfully.")
            return results, title
        except Exception as e:
            logging.error(f"Error processing PDF file: {e}", exc_info=True)
            raise


class HybridRetriever(BaseRetriever):
    """
    A hybrid retriever that combines results from vector-based and BM25 retrieval methods.
    Inherits from BaseRetriever.
    
    This class uses two different retrieval methods and merges their results to provide a
    comprehensive set of documents in response to a query. It ensures diversity in the
    retrieved documents by leveraging the strengths of both retrieval methods.

    Attributes:
        vector_retriever: An instance of a vector-based retriever.
        bm25_retriever: An instance of a BM25 retriever.

    Methods:
        __init__(vector_retriever, bm25_retriever): Initializes the HybridRetriever with vector and BM25 retrievers.
        _retrieve(query, **kwargs): Performs the retrieval operation by combining results from both retrievers.
        _combine_results(bm25_nodes, vector_nodes): Combines and de-duplicates the results from both retrievers.
    """

    def __init__(self, vector_retriever, bm25_retriever):
        super().__init__()
        self.vector_retriever = vector_retriever
        self.bm25_retriever = bm25_retriever
        logger.info("HybridRetriever initialized with vector and BM25 retrievers.")

    def _retrieve(self, query: str, **kwargs) -> List:
        """
        Retrieves and combines results from both vector and BM25 retrievers.

        Args:
            query: The query string for document retrieval.
            **kwargs: Additional keyword arguments for retrieval.

        Returns:
            List: Combined list of unique nodes retrieved from both methods.
        """
        logger.info(f"Retrieving documents for query: {query}")
        try:
            bm25_nodes = self.bm25_retriever.retrieve(query, **kwargs)
            vector_nodes = self.vector_retriever.retrieve(query, **kwargs)
            combined_nodes = self._combine_results(bm25_nodes, vector_nodes)

            logger.info(f"Retrieved {len(combined_nodes)} unique nodes combining vector and BM25 retrievers.")
            return combined_nodes
        except Exception as e:
            logger.error(f"Error in retrieval: {e}")
            raise

    @staticmethod
    def _combine_results(bm25_nodes: List, vector_nodes: List) -> List:
        """
        Combines and de-duplicates results from BM25 and vector retrievers.

        Args:
            bm25_nodes: Nodes retrieved from BM25 retriever.
            vector_nodes: Nodes retrieved from vector retriever.

        Returns:
            List: Combined list of unique nodes.
        """
        node_ids: Set = set()
        combined_nodes = []

        for node in bm25_nodes + vector_nodes:
            if node.node_id not in node_ids:
                combined_nodes.append(node)
                node_ids.add(node.node_id)

        return combined_nodes

        

class PDFQueryEngine:
    """
    A class to handle the process of setting up a query engine and performing queries on PDF documents.

    This class encapsulates the functionality of creating prompt templates, embedding models, service contexts,
    indexes, hybrid retrievers, response synthesizers, and executing queries on the set up engine.

    Attributes:
        documents (List): A list of documents to be indexed.
        llm (Language Model): The language model to be used for embeddings and queries.
        qa_prompt_tmpl (str): Template for creating query prompts.
        queries (List[str]): List of queries to be executed.

    Methods:
        setup_query_engine(): Sets up the query engine with all necessary components.
        execute_queries(): Executes the predefined queries and prints the results.
    """

    def __init__(self, documents: List[Any], llm: Any, embed_model: Any, qa_prompt_tmpl: Any):
        
        self.documents = documents
        self.llm = llm
        self.embed_model = embed_model
        self.qa_prompt_tmpl = qa_prompt_tmpl
        self.base_utils = base_utils()
        self.config_manager = ConfigManager()
        
        
    
        logger.info("PDFQueryEngine initialized.")

    def format_example(self, example):
        """
        Formats a few-shot example into a string.

        Args:
            example (dict): A dictionary containing 'query', 'score', and 'reasoning' for the few-shot example.

        Returns:
            str: Formatted few-shot example text.
        """
        return "Example:\nQuery: {}\nScore: {}\nReasoning: {}\n".format(
            example['query'], example['score'], example['reasoning']
        )


    def setup_query_engine(self):
        """
        Sets up the query engine by initializing and configuring the embedding model, service context, index,
        hybrid retriever (combining vector and BM25 retrievers), and the response synthesizer.

        Args:
            embed_model: The embedding model to be used.
            service_context: The context for providing services to the query engine.
            index: The index used for storing and retrieving documents.
            hybrid_retriever: The retriever that combines vector and BM25 retrieval methods.
            response_synthesizer: The synthesizer for generating responses to queries.

        Returns:
            Any: The configured query engine.
        """
        client = qdrant_client.QdrantClient(
            # you can use :memory: mode for fast and light-weight experiments,
            # it does not require to have Qdrant deployed anywhere
            # but requires qdrant-client >= 1.1.1
            location=":memory:"
            # otherwise set Qdrant instance address with:
            # uri="http://<host>:<port>"
            # set API KEY for Qdrant Cloud
            # api_key="<qdrant-api-key>",
            )
        try:
            logger.info("Initializing the service context for query engine setup.")
            service_context = ServiceContext.from_defaults(llm=self.llm, embed_model=self.embed_model)
            vector_store = QdrantVectorStore(client=client, collection_name="med_library")
            storage_context = StorageContext.from_defaults(vector_store=vector_store)

            logger.info("Creating an index from documents.")
            index = VectorStoreIndex.from_documents(documents=self.documents, storage_context=storage_context, service_context=service_context)
            nodes = service_context.node_parser.get_nodes_from_documents(self.documents)

            logger.info("Setting up vector and BM25 retrievers.")
            vector_retriever = index.as_retriever(similarity_top_k=3)
            bm25_retriever = BM25Retriever.from_defaults(nodes=nodes, similarity_top_k=3)
            hybrid_retriever = HybridRetriever(vector_retriever, bm25_retriever)
        
            logger.info("Configuring the response synthesizer with the prompt template.")
            qa_prompt = PromptTemplate(self.qa_prompt_tmpl)
            response_synthesizer = get_response_synthesizer(
                service_context=service_context,
                text_qa_template=qa_prompt,
                response_mode="compact",
            )

            logger.info("Assembling the query engine with reranker and synthesizer.")
            reranker = SentenceTransformerRerank(top_n=3, model="BAAI/bge-reranker-base") 
            query_engine = RetrieverQueryEngine.from_args(
                retriever=hybrid_retriever,
                node_postprocessors=[reranker],
                response_synthesizer=response_synthesizer,
            )

            logger.info("Query engine setup complete.")
            return query_engine
        except Exception as e:
            logger.error(f"Error during query engine setup: {e}")
            raise

    def evaluate_with_llm(self, reg_result: Any, peer_result: Any, guidelines_result: Any, queries: List[str]) -> Tuple[int, List[int], int, float, List[str]]:
        """
        Evaluate documents using a language model based on various criteria.
        Args:
            reg_result (Any): Result related to registration.
            peer_result (Any): Result related to peer review.
            guidelines_result (Any): Result related to following guidelines.
            queries (List[str]): A list of queries to be processed.
        Returns:
            Tuple[int, List[int], int, float, List[str]]: A tuple containing the total score, a list of scores per criteria.
        """
    
        logger.info("Starting evaluation with LLM.")
        self.config_manager.load_config("few_shot", "few_shot.json")
        query_engine = self.setup_query_engine()

        total_score = 0
        criteria_met = 0
        reasoning = []
    
        for j, query in enumerate(queries):
            # Handle special cases based on the value of j and other conditions
            if j == 1 and reg_result:
                extracted_data = {"score": 1, "reasoning": reg_result[0]}
            elif j == 2 and guidelines_result:
                extracted_data = {"score": 1, "reasoning": "The article is published in a journal following EQUATOR-NETWORK reporting guidelines"}
            elif j == 8 and (guidelines_result or peer_result):
                extracted_data = {"score": 1, "reasoning": "The article is published in a peer-reviewed journal."}
            else:
                
                # Execute the query
                result = query_engine.query(query).response
                extracted_data = self.base_utils.extract_score_reasoning(result)


            # Validate and accumulate the scores
            extracted_data_score = 0 if extracted_data.get("score") is None else int(extracted_data.get("score"))
            if extracted_data_score > 0:
                criteria_met += 1
            reasoning.append(extracted_data["reasoning"])
            total_score += extracted_data_score

        score_percentage = (float(total_score) / len(queries)) * 100
        logger.info("Evaluation completed.")
        return total_score, criteria_met, score_percentage, reasoning
        


class MixtralLLM(CustomLLM):
    """
    A custom language model class for interfacing with the Hugging Face API, specifically using the Mixtral model.

    Attributes:
        context_window (int): Number of tokens used for context during inference.
        num_output (int): Number of tokens to generate as output.
        temperature (float): Sampling temperature for token generation.
        model_name (str): Name of the model on Hugging Face's model hub.
        api_key (str): API key for authenticating with the Hugging Face API.

    Methods:
        metadata: Retrieves metadata about the model.
        do_hf_call: Makes an API call to the Hugging Face model.
        complete: Generates a complete response for a given prompt.
        stream_complete: Streams a series of token completions for a given prompt.
    """
    context_window: int = Field(..., description="Number of tokens used for context during inference.")
    num_output: int = Field(..., description="Number of tokens to generate as output.")
    temperature: float = Field(..., description="Sampling temperature for token generation.")
    model_name: str = Field(..., description="Name of the model on Hugging Face's model hub.")
    api_key: str = Field(..., description="API key for authenticating with the Hugging Face API.")


    @property
    def metadata(self) -> LLMMetadata:
        """
        Retrieves metadata for the Mixtral LLM.

        Returns:
            LLMMetadata: An object containing metadata such as context window, number of outputs, and model name.
        """
        return LLMMetadata(
            context_window=self.context_window,
            num_output=self.num_output,
            model_name=self.model_name,
        )

    def do_hf_call(self, prompt: str) -> str:
        """
        Makes an API call to the Hugging Face model and retrieves the generated response.

        Args:
            prompt (str): The input prompt for the model.

        Returns:
            str: The text generated by the model in response to the prompt.
        
        Raises:
            Exception: If the API call fails or returns an error.
        """
        data = {
            "inputs": prompt,
            "parameters": {"Temperature": self.temperature}
        }

        # Makes a POST request to the Hugging Face API to get the model's response
        response = requests.post(
            f'https://api-inference.huggingface.co/models/{self.model_name}',
            headers={
                'authorization': f'Bearer {self.api_key}',
                'content-type': 'application/json',
            },
            json=data,
            stream=True
        )

        # Checks for a successful response and parses the generated text
        if response.status_code != 200 or not response.json() or 'error' in response.json():
            print(f"Error: {response}")
            return "Unable to answer for technical reasons."
        full_txt = response.json()[0]['generated_text']
        # Finds the section of the text following the context separator
        offset = full_txt.find("---------------------")
        ss = full_txt[offset:]
        # Extracts the actual answer from the response
        offset = ss.find("Answer:")
        return ss[offset+7:].strip()

    
    @llm_completion_callback()
    def complete(self, prompt: str, **kwargs: Any) -> CompletionResponse:
        """
        Generates a complete response for a given prompt using the Hugging Face API.

        Args:
            prompt (str): The input prompt for the model.
            **kwargs: Additional keyword arguments for the completion.

        Returns:
            CompletionResponse: The complete response from the model.
        """
        response = self.do_hf_call(prompt)
        return CompletionResponse(text=response)

    
    @llm_completion_callback()
    def stream_complete(
            self, prompt: str, **kwargs: Any
    ) -> CompletionResponseGen:
        """
        Streams a series of token completions as a response for the given prompt.

        This method is useful for streaming responses where each token is generated sequentially.

        Args:
            prompt (str): The input prompt for the model.
            **kwargs: Additional keyword arguments for the streaming completion.

        Yields:
            CompletionResponseGen: A generator yielding each token in the completion response.
        """
        # Yields a stream of tokens as the completion response for the given prompt
        response = ""
        for token in self.do_hf_call(prompt):
            response += token
            yield CompletionResponse(text=response, delta=token)



class KeywordSearch():
    def __init__(self, chunks):
        self.chunks = chunks
    
    def find_journal_name(self, response: str, journal_list: list) -> str:
        """
        Searches for a journal name in a given response string.

        This function iterates through a list of known journal names and checks if any of these
        names are present in the response string. It returns the first journal name found in the
        response. If no journal names from the list are found in the response, a default message
        indicating that the journal name was not found is returned.

        Args:
            response (str): The response string to search for a journal name.
            journal_list (list): A list of journal names to search within the response.

        Returns:
            str: The first journal name found in the response, or a default message if no journal name is found.
        """
        response_lower = response.lower()
        for journal in journal_list:
            journal_lower = journal.lower()
            
            if journal_lower in response_lower:
                print(journal_lower,response_lower)
                return True
        
        return False

    def check_registration(self):
        """
        Check chunks of text for various registration numbers or URLs of registries.
        Returns the sentence containing a registration number, or if not found,
        returns chunks containing registry URLs.

        Args:
        chunks (list of str): List of text chunks to search.

        Returns:
        list of str: List of matching sentences or chunks, or an empty list if no matches are found.
        """

        # Patterns for different registration types
        patterns = {
            "NCT": r"\(?(NCT#?\s*(No\s*)?)(\d{8})\)?",
            "ISRCTN": r"(ISRCTN\d{8})",
            "EudraCT": r"(\d{4}-\d{6}-\d{2})",
            "UMIN-CTR": r"(UMIN\d{9})",
            "CTRI": r"(CTRI/\d{4}/\d{2}/\d{6})"
        }

        # Registry URLs
        registry_urls = [
            "www.anzctr.org.au",
            "anzctr.org.au",
            "www.clinicaltrials.gov",
            "clinicaltrials.gov",
            "www.ISRCTN.org",
            "ISRCTN.org",
            "www.umin.ac.jp/ctr/index/htm",
            "umin.ac.jp/ctr/index/htm",
            "www.onderzoekmetmensen.nl/en",
            "onderzoekmetmensen.nl/en",
            "eudract.ema.europa.eu",
            "www.eudract.ema.europa.eu"
            ]
    

        # Check each chunk for registration numbers
        for chunk in self.chunks:
            # Split chunk into sentences
            sentences = re.split(r'(?<=[.!?]) +', chunk)

            # Check each sentence for any registration number
            for sentence in sentences:
                for pattern in patterns.values():
                    if re.search(pattern, sentence):
                        return [sentence]  # Return immediately if a registration number is found

        # If no registration number found, check for URLs in chunks
        matching_chunks = []
        for chunk in self.chunks:
            if any(url in chunk for url in registry_urls):
                matching_chunks.append(chunk)

        return matching_chunks

    

class StringExtraction():

    """
    A class to handle the the process of extraction of query string from complete LLM responses.

    This class encapsulates the functionality of extracting original ground truth from a labelled data csv and query strings from responses. Please note that
    LLMs may generate different formatted answers based on different models or different prompting technique. In such cases, extract_original_prompt may not give 
    satisfactory results. Best case scenario will be write your own string extraction method in such cases.

    
    Methods:
        extract_original_prompt(): 
        extraction_ground_truth(): 
    """

    def extract_original_prompt(self,result):
        r1 = result.response.strip().split("\n")
        binary_response = ""
        explanation_response = ""
        for r in r1:
            if binary_response == "" and (r.find("Yes") >= 0 or r.find("No") >= 0):
                binary_response = r
            elif r.find("Reasoning:") >= 0:
                cut = r.find(":")
                explanation_response += r[cut+1:].strip()
            
        return binary_response,explanation_response

    def extraction_ground_truth(self,paper_name,labelled_data):
        id = int(paper_name[paper_name.find("_")+1:paper_name.find(".pdf")])
        id_row = labelled_data[labelled_data["id"] == id]
        ground_truth = id_row.iloc[:,2:11].values.tolist()[0]
        binary_ground_truth = []
        explanation_ground_truth = []
        for g in ground_truth:
            if len(g) > 0:
                binary_ground_truth.append("Yes")
                explanation_ground_truth.append(g)
            else:
                binary_ground_truth.append("No")
                explanation_ground_truth.append("The article does not provide any relevant information.")
        return binary_ground_truth,explanation_ground_truth
    

  
class EvaluationMetrics():
    """

    This class encapsulates the evaluation methods that have been used in the project.

    Attributes:
        explanation_response = a list of detailed response from the LLM model corresponding to each query
        explanation_ground_truth = the list of ground truth corresponding to each query

    Methods:
        metric_cosine_similairty(): Sets up the query engine with all necessary components.
        metric_rouge(): Executes the predefined queries and prints the results.
        metric_binary_accuracy():
    """


    def __init__(self,explanation_response,explanation_ground_truth,embedding_model):
        self.explanation_response = explanation_response
        self.explanation_ground_truth = explanation_ground_truth
        self.embedding_model = embedding_model
    
    def metric_cosine_similarity(self):
        ground_truth_embedding = self.embedding_model.encode(self.explanation_ground_truth)
        explanation_response_embedding = self.embedding_model.encode(self.explanation_response)
        return np.diag(cosine_similarity(ground_truth_embedding,explanation_response_embedding))
    
    def metric_rouge(self):
        rouge = evaluate.load("rouge")
        results = rouge.compute(predictions = self.explanation_response,references = self.explanation_ground_truth)
        return results 

    def binary_accuracy(self,binary_response,binary_ground_truth):
        count = 0
        if len(binary_response) != len(binary_ground_truth):
            return "Arrays which are to be compared has different lengths."
        else:
            for i in range(len(binary_response)):
                if binary_response[i] == binary_ground_truth[i]:
                    count += 1
            return np.round(count/len(binary_response),2)