process.py

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_google_genai import ChatGoogleGenerativeAI
from langchain_openai import ChatOpenAI
from pdf2image import convert_from_path
from prompt import *
from table_detector import detection_transform, device, model, ocr, outputs_to_objects

import io
import json
import os
import pandas as pd
import re
import torch

load_dotenv()

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]
}

class Process():

    def __init__(self, llm):

        if llm.startswith('gpt'):
            self.llm = ChatOpenAI(temperature=0, model_name=llm)
        elif llm.startswith('gemini'):
            self.llm = ChatGoogleGenerativeAI(temperature=0, model=llm)
        else:
            self.llm = ChatOpenAI(temperature=0, model_name=llm, api_key=os.environ['PERPLEXITY_API_KEY'], base_url="https://api.perplexity.ai")

    def get_entity(self, data):

        chunks, types = data

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

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

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

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

        return eval(result)

    def get_table(self, path):

        images = convert_from_path(path)
        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)

        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 = df_table.fillna('')

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

            result = self.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(genes, snps, diseases)
        return genes, snps, diseases