process.py

from datetime import datetime
from dotenv import load_dotenv
from img2table.document import Image
from langchain.chains.combine_documents.map_reduce import MapReduceDocumentsChain
from langchain.chains.combine_documents.reduce import ReduceDocumentsChain
from langchain.chains.combine_documents.stuff import StuffDocumentsChain
from langchain.chains.llm import LLMChain
from langchain.prompts import PromptTemplate
from langchain_openai import ChatOpenAI
from pdf2image import convert_from_path
from prompt import prompt_entity_gsd_chunk, prompt_entity_gsd_combine, prompt_entity_summ_chunk, prompt_entity_summ_combine, prompt_entities_chunk, prompt_entities_combine, prompt_entity_one_chunk, prompt_table, prompt_validation
from table_detector import detection_transform, device, model, ocr, outputs_to_objects

import google.generativeai as genai
import io
import json
import os
import pandas as pd
import re
import torch

load_dotenv()
genai.configure(api_key=os.environ['GOOGLE_API_KEY'])

llm = ChatOpenAI(temperature=0, model_name="gpt-4-turbo")
llm_p = ChatOpenAI(temperature=0, model_name="llama-3-sonar-large-32k-chat", api_key=os.environ['PERPLEXITY_API_KEY'], base_url="https://api.perplexity.ai")
llm_g = genai.GenerativeModel(model_name='gemini-1.5-pro-latest')

prompts = {
    'gsd': [prompt_entity_gsd_chunk, prompt_entity_gsd_combine],
    'summ': [prompt_entity_summ_chunk, prompt_entity_summ_combine],
    'all': [prompt_entities_chunk, prompt_entities_combine]
}

def get_entity(data):

    chunks, types = data

    map_template = prompts[types][0]
    map_prompt = PromptTemplate.from_template(map_template)
    map_chain = LLMChain(llm=llm, prompt=map_prompt)

    reduce_template = prompts[types][1]
    reduce_prompt = PromptTemplate.from_template(reduce_template)
    reduce_chain = LLMChain(llm=llm, prompt=reduce_prompt)

    combine_chain = StuffDocumentsChain(
        llm_chain=reduce_chain, document_variable_name="doc_summaries"
    )

    reduce_documents_chain = ReduceDocumentsChain(
        combine_documents_chain=combine_chain,
        collapse_documents_chain=combine_chain,
        token_max=100000,
    )

    map_reduce_chain = MapReduceDocumentsChain(
        llm_chain=map_chain,
        reduce_documents_chain=reduce_documents_chain,
        document_variable_name="docs",
        return_intermediate_steps=False,
    )

    result = map_reduce_chain.invoke(chunks)['output_text']
    print(types)
    print(result)
    if types != 'summ':
        result = re.findall('(\{[^}]+\})', result)[0]
        return eval(result)
    
    return result

def get_entity_one(chunks):

    result = llm.invoke(prompt_entity_one_chunk.format(chunks)).content

    print('One')
    print(result)
    result = re.findall('(\{[^}]+\})', result)[0]

    return eval(result)

def get_table(path):

    start_time = datetime.now()
    images = convert_from_path(path)
    print('PDF to Image', round((datetime.now().timestamp() - start_time.timestamp()) / 60, 2), "minutes")
    tables = []

    # Loop pages
    for image in images:

        pixel_values = detection_transform(image).unsqueeze(0).to(device)
        with torch.no_grad():
            outputs = model(pixel_values)

        id2label = model.config.id2label
        id2label[len(model.config.id2label)] = "no object"
        detected_tables = outputs_to_objects(outputs, image.size, id2label)

        # Loop table in page (if any)
        for idx in range(len(detected_tables)):
            cropped_table = image.crop(detected_tables[idx]["bbox"])
            if detected_tables[idx]["label"] == 'table rotated':
                cropped_table = cropped_table.rotate(270, expand=True)

            # TODO: what is the perfect threshold?
            if detected_tables[idx]['score'] > 0.9:
                print(detected_tables[idx])
                tables.append(cropped_table)

    print('Detect table from image', round((datetime.now().timestamp() - start_time.timestamp()) / 60, 2), "minutes")
    genes = []
    snps = []
    diseases = []

    # Loop tables
    for table in tables:

        buffer = io.BytesIO()
        table.save(buffer, format='PNG')
        image = Image(buffer)
        
        # Extract to dataframe
        extracted_tables = image.extract_tables(ocr=ocr, implicit_rows=True, borderless_tables=True, min_confidence=0)

        if len(extracted_tables) == 0:
            continue

        # Combine multiple dataframe
        df_table = extracted_tables[0].df
        for extracted_table in extracted_tables[1:]:
            df_table = pd.concat([df_table, extracted_table.df]).reset_index(drop=True)

        df_table.loc[0] = df_table.loc[0].fillna('')

        # Identify multiple rows (in dataframe) as one row (in image)
        rows = []
        indexes = []
        for i in df_table.index:
            if not df_table.loc[i].isna().any():
                if len(indexes) > 0:
                    rows.append(indexes)
                indexes = []
            indexes.append(i)
        rows.append(indexes)

        df_table_cleaned = pd.DataFrame(columns=df_table.columns)
        for row in rows:
            row_str = df_table.loc[row[0]]
            for idx in row[1:]:
                row_str += ' ' + df_table.loc[idx].fillna('')
            row_str = row_str.str.strip()
            df_table_cleaned.loc[len(df_table_cleaned)] = row_str

        # Ask LLM with JSON data
        json_table = df_table_cleaned.to_json(orient='records')
        str_json_table = json.dumps(json.loads(json_table), indent=2)

        result = llm.invoke(prompt_table.format(str_json_table)).content
        print('table')
        print(result)
        result = result[result.find('['):result.rfind(']')+1]
        try:
            result = eval(result)
        except SyntaxError:
            result = []

        for res in result:
            res_gene = res['Genes']
            res_snp = res['SNPs']
            res_disease = res['Diseases']

            for snp in res_snp:
                genes.append(res_gene)
                snps.append(snp)
                diseases.append(res_disease)

    print('OCR table to extract', round((datetime.now().timestamp() - start_time.timestamp()) / 60, 2), "minutes")
    print(genes, snps, diseases)
    
    return genes, snps, diseases

def validate(df):

    df = df[df['Genes'].notna()].reset_index(drop=True)
    df = df.fillna('')
    df['Genes'] = df['Genes'].str.upper()
    df['SNPs'] = df['SNPs'].str.lower()

    # Check if there is two gene names
    sym = ['-', '/', '|']
    for i in df.index:
        gene = df.loc[i, 'Genes']
        for s in sym:
            if s in gene:
                genes = gene.split(s)
                df.loc[i + 0.5] = df.loc[i]
                df = df.sort_index().reset_index(drop=True)
                df.loc[i, 'Genes'], df.loc[i + 1, 'Genes'] = genes[0], genes[1]

    # Check if there is SNPs without 'rs'
    for i in df.index:
        safe = True
        snp = df.loc[i, 'SNPs']
        if re.fullmatch('rs(\d)+|', snp):
            pass
        elif re.fullmatch('ts(\d)+', snp):
            snp = 'r' + snp[1:]
        elif re.fullmatch('s(\d)+', snp):
            snp = 'r' + snp
        elif re.fullmatch('(\d)+', snp):
            snp = 'rs' + snp
        else:
            safe = False
            df = df.drop(i)
            
        if safe:
            df.loc[i, 'SNPs'] = snp

    df.reset_index(drop=True, inplace=True)

    # Validate genes and diseases with LLM
    json_table = df[['Genes', 'SNPs', 'Diseases']].to_json(orient='records')
    str_json_table = json.dumps(json.loads(json_table), indent=2)

    result = llm_p.invoke(input=prompt_validation.format(str_json_table)).content
    print('val')
    print(result)

    result = result[result.find('['):result.rfind(']')+1]
    try:
        result = eval(result)
    except SyntaxError:
        result = []

    df_val = pd.DataFrame(result)
    df_val = df_val.merge(df.head(1).drop(['Genes', 'SNPs', 'Diseases'], axis=1), 'cross')

    # TODO: How to validate genes and SNPs with ground truth?

    return df, df_val