run.py

###########################################################################################
# Title:  Gradio Interface to LLM-chatbot with dynamic RAG-funcionality and ChromaDB
# Author: Andreas Fischer
# Date:   October 10th, 2024
# Last update: October 10th, 2024
##########################################################################################

import os
import chromadb
from datetime import datetime
from chromadb import Documents, EmbeddingFunction, Embeddings
from chromadb.utils import embedding_functions
from transformers import AutoTokenizer, AutoModel
import torch
jina = AutoModel.from_pretrained('jinaai/jina-embeddings-v2-base-de', trust_remote_code=True, torch_dtype=torch.bfloat16)
#jira.save_pretrained("jinaai_jina-embeddings-v2-base-de")   
device='cuda' if torch.cuda.is_available() else 'cpu'
#device='cpu' #'cuda' if torch.cuda.is_available() else 'cpu'
jina.to(device) #cuda:0
print(device)

class JinaEmbeddingFunction(EmbeddingFunction):
  def __call__(self, input: Documents) -> Embeddings:    
    embeddings = jina.encode(input) #max_length=2048
    return(embeddings.tolist())

dbPath = "/home/af/Schreibtisch/Code/gradio/Chroma/db" 
onPrem = True if(os.path.exists(dbPath)) else False 
if(onPrem==False): dbPath="/home/user/app/db"

#onPrem=True  # uncomment to override automatic detection
print(dbPath)
path=dbPath
client = chromadb.PersistentClient(path=path)
print(client.heartbeat()) 
print(client.get_version())  
print(client.list_collections()) 
jina_ef=JinaEmbeddingFunction()
embeddingModel=jina_ef


from huggingface_hub import InferenceClient
import gradio as gr
import json
inferenceClient = InferenceClient(
    "mistralai/Mixtral-8x7B-Instruct-v0.1"
    #"mistralai/Mistral-7B-Instruct-v0.1"
)
def format_prompt(message, history):
  prompt = "<s>"
  #for user_prompt, bot_response in history:
  #  prompt += f"[INST] {user_prompt} [/INST]"
  #  prompt += f" {bot_response}</s> "
  prompt += f"[INST] {message} [/INST]"
  return prompt



from pypdf import PdfReader
import ocrmypdf
def convertPDF(pdf_file, allow_ocr=False):
    reader = PdfReader(pdf_file)
    full_text = ""
    page_list = []       
    def extract_text_from_pdf(reader):
        full_text = ""
        page_list = []
        page_count = 1
        for idx, page in enumerate(reader.pages):
            text = page.extract_text()
            if len(text) > 0:
                page_list.append(text)
                #full_text += f"---- Page {idx} ----\n" + text + "\n\n"
                page_count += 1    
        return full_text.strip(), page_count, page_list
    # Check if there are any images
    image_count = sum(len(page.images) for page in reader.pages)
    # If there are images and not much content, perform OCR on the document
    if allow_ocr:
        print(f"{image_count} Images") 
        if image_count > 0 and len(full_text) < 1000:
            out_pdf_file = pdf_file.replace(".pdf", "_ocr.pdf")
            ocrmypdf.ocr(pdf_file, out_pdf_file, force_ocr=True)        
            reader = PdfReader(out_pdf_file)
    # Extract text:
    full_text, page_count, page_list = extract_text_from_pdf(reader)
    l = len(page_list)
    print(f"{l} Pages")
    # Extract metadata
    metadata = {
        "author": reader.metadata.author,
        "creator": reader.metadata.creator,
        "producer": reader.metadata.producer,
        "subject": reader.metadata.subject,
        "title": reader.metadata.title,
        "image_count": image_count,
        "page_count": page_count,
        "char_count": len(full_text),
    }    
    return page_list, full_text, metadata

def split_with_overlap(text,chunk_size=3500, overlap=700):
 chunks=[]
 step=max(1,chunk_size-overlap)
 for i in range(0,len(text),step):
   end=min(i+chunk_size,len(text))
   #chunk = text[i:i+chunk_size]
   chunks.append(text[i:end])
 return chunks

def add_doc(path):
  print("def add_doc!")
  print(path)
  if(str.lower(path).endswith(".pdf")):
      doc=convertPDF(path)
      doc="\n\n".join(doc[0]) 
      gr.Info("PDF uploaded, start Indexing!")
  else:
      gr.Info("Error: Only pdfs are accepted!")
  client = chromadb.PersistentClient(path="output/general_knowledge")
  print(str(client.list_collections()))
  #global collection
  dbName="test"
  if("name="+dbName in str(client.list_collections())): 
    client.delete_collection(name=dbName) 
  collection = client.create_collection(
    dbName,
    embedding_function=embeddingModel,
    metadata={"hnsw:space": "cosine"})
  corpus=split_with_overlap(doc,3500,700) 
  print(len(corpus))
  then = datetime.now()
  x=collection.get(include=[])["ids"]
  print(len(x))
  if(len(x)==0):
    chunkSize=40000
    for i in range(round(len(corpus)/chunkSize+0.5)): #0 is first batch, 3 is last (incomplete) batch given 133497 texts
      print("embed batch "+str(i)+" of "+str(round(len(corpus)/chunkSize+0.5)))
      ids=list(range(i*chunkSize,(i*chunkSize+chunkSize)))
      batch=corpus[i*chunkSize:(i*chunkSize+chunkSize)]
      textIDs=[str(id) for id in ids[0:len(batch)]]
      ids=[str(id+len(x)+1) for id in ids[0:len(batch)]] # id refers to chromadb-unique ID      
      collection.add(documents=batch, ids=ids, 
        metadatas=[{"date": str("2024-10-10")} for b in batch]) #"textID":textIDs, "id":ids, 
      print("finished batch "+str(i)+" of "+str(round(len(corpus)/40000+0.5)))  
  now = datetime.now()
  gr.Info(f"Indexing complete!")
  print(now-then) #zu viel GB für sentences (GPU), bzw. 0:00:10.375087 für chunks
  return(collection)

#split_with_overlap("test me if you can",2,1)

import gradio as gr
import re  
def multimodalResponse(message,history,headerPattern,sentenceWiseSplitting):
  print("def multimodal response!")
  length=str(len(history))
  query=message["text"]
  if(len(message["files"])>0): # is there at least one file attached?
    collection=add_doc(message["files"][0])
  client = chromadb.PersistentClient(path="output/general_knowledge")
  print(str(client.list_collections()))
  x=collection.get(include=[])["ids"]  
  context=collection.query(query_texts=[query], n_results=1)
  print(str(context))    
  #context=["<context "+str(i+1)+">\n"+c+"\n</context "+str(i+1)+">" for i, c in enumerate(retrievedTexts)]
  #context="\n\n".join(context)
  #return context
  if temperature < 1e-2: temperature = 1e-2
  top_p = float(top_p)
  generate_kwargs = dict(
        temperature=float(0.9),
        max_new_tokens=5000,
        top_p=0.95,
        repetition_penalty=1.0,
        do_sample=True,
        seed=42,
  )
  system="Given the following conversation, relevant context, and a follow up question, "+\
  "reply with an answer to the current question the user is asking. "+\
  "Return only your response to the question given the above information "+\
  "following the users instructions as needed.\n\nContext:"+\
  str(context)
  print(system)
  formatted_prompt = format_prompt(system+"\n"+prompt, history)
  stream = client.text_generation(formatted_prompt, **generate_kwargs, stream=True, details=True, return_full_text=False)
  output = ""
  for response in stream:
    output += response.token.text
    yield output
  #output=output+"\n\n<br><details open><summary><strong>Sources</strong></summary><br><ul>"+ "".join(["<li>" + s + "</li>" for s in combination])+"</ul></details>"
  yield output

i=gr.ChatInterface(multimodalResponse,
  title="pdfChatbot",
  multimodal=True,
  additional_inputs=[
    gr.Dropdown(
      info="select retrieval version",
      choices=["1","2","3"],
      value=["1"],
      label="Retrieval Version")])
i.launch() #allowed_paths=["."])