app.py

import io
import os
import pandas as pd
import streamlit as st

from datetime import datetime
from langchain_community.document_loaders.pdf import PyPDFLoader
from langchain_core.documents.base import Document
from langchain_text_splitters import TokenTextSplitter
from process import get_entity, get_entity_one, get_table, validate
from tempfile import NamedTemporaryFile
from stqdm import stqdm
from threading import Thread

class CustomThread(Thread):
    def __init__(self, func, chunk):
        super().__init__()
        self.func = func
        self.chunk = chunk
        self.result = ''

    def run(self):
        self.result = self.func(self.chunk)

buffer = io.BytesIO()

st.cache_data()
st.set_page_config(page_title="NutriGenMe Paper Extractor")
st.title("NutriGenMe - Paper Extraction")
st.markdown("<div style='text-align: left; color: white; font-size: 16px'>In its latest version, the app is equipped to extract essential information from papers, including tables in both horizontal and vertical orientations, images, and text exclusively.</div><br>", unsafe_allow_html=True)

uploaded_files = st.file_uploader("Upload Paper(s) here :", type="pdf", accept_multiple_files=True)

chunk_option = st.selectbox(
    'Tokens amounts per process :',
    (32000, 16000, 8000, 0), key='table_hv'
)
chunk_overlap = 0

if uploaded_files:
    journals = []
    parseButtonHV = st.button("Get Result", key='table_HV')

    if parseButtonHV:
        with st.status("Extraction in progress ...", expanded=True) as status:
            start_time = datetime.now()

            csv = pd.DataFrame()
            for uploaded_file in stqdm(uploaded_files):
                with NamedTemporaryFile(dir='.', suffix=".pdf", delete=eval(os.getenv('DELETE_TEMP_PDF', 'True'))) as pdf:
                    pdf.write(uploaded_file.getbuffer())
                    loader = PyPDFLoader(pdf.name)
                    pages = loader.load()

                    chunk_size = 120000
                    chunk_overlap = 0
                    docs = pages

                    if chunk_option:
                        docs = [Document('\n'.join([page.page_content for page in pages]))]
                        docs[0].metadata = {'source': pages[0].metadata['source']}

                        chunk_size = chunk_option
                        chunk_overlap = int(0.25 * chunk_size)

                    text_splitter = TokenTextSplitter.from_tiktoken_encoder(
                        chunk_size=chunk_size, chunk_overlap=chunk_overlap
                    )
                    chunks = text_splitter.split_documents(docs)

                    threads = []
                    threads.append(CustomThread(get_entity, (chunks, 'gsd')))
                    threads.append(CustomThread(get_entity, (chunks, 'summ')))
                    threads.append(CustomThread(get_entity, (chunks, 'all')))
                    threads.append(CustomThread(get_entity_one, [c.page_content for c in chunks[:1]]))
                    threads.append(CustomThread(get_table, pdf.name))

                    [t.start() for t in threads]
                    [t.join() for t in threads]
                    
                    result_gsd = threads[0].result
                    result_summ = threads[1].result
                    result = threads[2].result
                    result_one = threads[3].result
                    res_gene, res_snp, res_dis = threads[4].result

                    # Combine
                    result['Genes'] = res_gene + result_gsd['Genes']
                    result['SNPs'] = res_snp + result_gsd['SNPs']
                    result['Diseases'] = res_dis + result_gsd['Diseases']
                    result['Conclusion'] = result_summ
                    for k in result_one.keys():
                        result[k] = result_one[k]

                    if len(result['Genes']) == 0:
                        result['Genes'] = ['']
                    
                    num_rows = max(max(len(result['Genes']), len(result['SNPs'])), len(result['Diseases']))

                    # Adjust Genes, SNPs, Diseases
                    for k in ['Genes', 'SNPs', 'Diseases']:
                        while len(result[k]) < num_rows:
                            result[k].append('')

                        # Temporary handling
                        result[k] = result[k][:num_rows]

                    # Key Column
                    result = {key: value if isinstance(value, list) else [value] * num_rows for key, value in result.items()}

                    dataframe = pd.DataFrame(result)
                    dataframe = dataframe[['Genes', 'SNPs', 'Diseases', 'Title', 'Authors', 'Publisher Name', 'Publication Year', 'Population', 'Sample Size', 'Study Methodology', 'Study Level', 'Conclusion']]
                    dataframe.drop_duplicates(['Genes', 'SNPs'], inplace=True)
                    dataframe.reset_index(drop=True, inplace=True)
                    cleaned_dataframe = validate(dataframe)

                    end_time = datetime.now()
                    st.write("Success in ", round((end_time.timestamp() - start_time.timestamp()) / 60, 2), "minutes")

                    st.dataframe(cleaned_dataframe)
                    with pd.ExcelWriter(buffer, engine='xlsxwriter') as writer:
                        cleaned_dataframe.to_excel(writer, sheet_name='Result')
                        dataframe.to_excel(writer, sheet_name='Original')
                        writer.close()

                    st.download_button(
                        label="Save Result",
                        data=buffer,
                        file_name=f"{uploaded_file.name.replace('.pdf', '')}_{chunk_option}.xlsx",
                        mime='application/vnd.ms-excel'
                    )