pages/4_qa_sources_v1.py

import datetime, os
from langchain.llms import OpenAI
from langchain.embeddings import OpenAIEmbeddings
import openai
import faiss
import streamlit as st
import feedparser
import urllib
import cloudpickle as cp
import pickle
from urllib.request import urlopen
from summa import summarizer
import numpy as np
import matplotlib.pyplot as plt

import requests
import json
from langchain.document_loaders import TextLoader
from langchain.indexes import VectorstoreIndexCreator
API_ENDPOINT = "https://api.openai.com/v1/chat/completions"

# openai.organization = st.secrets.openai.org
# openai.api_key = st.secrets.openai.api_key
openai.organization = st.secrets["org"]
openai.api_key = st.secrets["api_key"]
os.environ["OPENAI_API_KEY"] = openai.api_key

@st.cache_data
def get_feeds_data(url):
    # data = cp.load(urlopen(url))
    with open(url, "rb") as fp:
        data = pickle.load(fp)
    st.sidebar.success("Loaded data")
    return data

embeddings = OpenAIEmbeddings()

# feeds_link = "https://drive.google.com/uc?export=download&id=1-IPk1voyUM9VqnghwyVrM1dY6rFnn1S_"
# embed_link = "https://dl.dropboxusercontent.com/s/ob2betm29qrtb8v/astro_ph_ga_feeds_ada_embedding_18-Apr-2023.pkl?dl=0"
dateval = "27-Jun-2023"
feeds_link = "local_files/astro_ph_ga_feeds_upto_"+dateval+".pkl"
embed_link = "local_files/astro_ph_ga_feeds_ada_embedding_"+dateval+".pkl"
gal_feeds = get_feeds_data(feeds_link)
arxiv_ada_embeddings = get_feeds_data(embed_link)

@st.cache_data
def get_embedding_data(url):
    # data = cp.load(urlopen(url))
    with open(url, "rb") as fp:
        data = pickle.load(fp)
    st.sidebar.success("Fetched data from API!")
    return data

# url = "https://drive.google.com/uc?export=download&id=1133tynMwsfdR1wxbkFLhbES3FwDWTPjP"
url = "local_files/astro_ph_ga_embedding_"+dateval+".pkl"
e2d = get_embedding_data(url)
# e2d, _, _, _, _ = get_embedding_data(url)

ctr = -1
num_chunks = len(gal_feeds)
all_text, all_titles, all_arxivid, all_links, all_authors = [], [], [], [], []

for nc in range(num_chunks):

    for i in range(len(gal_feeds[nc].entries)):
        text = gal_feeds[nc].entries[i].summary
        text = text.replace('\n', ' ')
        text = text.replace('\\', '')
        all_text.append(text)
        all_titles.append(gal_feeds[nc].entries[i].title)
        all_arxivid.append(gal_feeds[nc].entries[i].id.split('/')[-1][0:-2])
        all_links.append(gal_feeds[nc].entries[i].links[1].href)
        all_authors.append(gal_feeds[nc].entries[i].authors)

d = arxiv_ada_embeddings.shape[1]                           # dimension
nb = arxiv_ada_embeddings.shape[0]                      # database size
xb = arxiv_ada_embeddings.astype('float32')
index = faiss.IndexFlatL2(d)
index.add(xb)

def run_simple_query(search_query = 'all:sed+fitting', max_results = 10, start = 0, sort_by = 'lastUpdatedDate', sort_order = 'descending'):
    """
        Query ArXiv to return search results for a particular query
        Parameters
        ----------
        query: str
            query term. use prefixes ti, au, abs, co, jr, cat, m, id, all as applicable.
        max_results: int, default = 10
            number of results to return. numbers > 1000 generally lead to timeouts
        start: int, default = 0
            start index for results reported. use this if you're interested in running chunks.
        Returns
        -------
        feed: dict
            object containing requested results parsed with feedparser
        Notes
        -----
            add functionality for chunk parsing, as well as storage and retreival
        """

    base_url = 'http://export.arxiv.org/api/query?';
    query = 'search_query=%s&start=%i&max_results=%i&sortBy=%s&sortOrder=%s' % (search_query,
                                                     start,
                                                     max_results,sort_by,sort_order)

    response = urllib.request.urlopen(base_url+query).read()
    feed = feedparser.parse(response)
    return feed

def find_papers_by_author(auth_name):

    doc_ids = []
    for doc_id in range(len(all_authors)):
        for auth_id in range(len(all_authors[doc_id])):
            if auth_name.lower() in all_authors[doc_id][auth_id]['name'].lower():
                print('Doc ID: ',doc_id, ' | arXiv: ', all_arxivid[doc_id], '| ', all_titles[doc_id],' | Author entry: ', all_authors[doc_id][auth_id]['name'])
                doc_ids.append(doc_id)

    return doc_ids

def faiss_based_indices(input_vector, nindex=10, yrmin = 1990, yrmax = 2024):
    xq = input_vector.reshape(-1,1).T.astype('float32')
    D, I = index.search(xq, nindex)
    return I[0], D[0]

def list_similar_papers_v2(model_data,
                        doc_id = [], input_type = 'doc_id',
                        show_authors = False, show_summary = False,
                        return_n = 10, yrmin = 1990, yrmax = 2024):

    arxiv_ada_embeddings, embeddings, all_titles, all_abstracts, all_authors = model_data

    if input_type == 'doc_id':
        print('Doc ID: ',doc_id,', title: ',all_titles[doc_id])
#         inferred_vector = model.infer_vector(train_corpus[doc_id].words)
        inferred_vector = arxiv_ada_embeddings[doc_id,0:]
        start_range = 1
    elif input_type == 'arxiv_id':
        print('ArXiv id: ',doc_id)
        arxiv_query_feed = run_simple_query(search_query='id:'+str(doc_id))
        if len(arxiv_query_feed.entries) == 0:
            print('error: arxiv id not found.')
            return
        else:
            print('Title: '+arxiv_query_feed.entries[0].title)
            inferred_vector = np.array(embeddings.embed_query(arxiv_query_feed.entries[0].summary))
        start_range = 0
    elif input_type == 'keywords':
        inferred_vector = np.array(embeddings.embed_query(doc_id))
        start_range = 0
    else:
        print('unrecognized input type.')
        return

    sims, dists = faiss_based_indices(inferred_vector, return_n+2, yrmin = 1990, yrmax = 2024)
    textstr = ''
    abstracts_relevant = []
    fhdrs = []

    for i in range(start_range,start_range+return_n):

        abstracts_relevant.append(all_text[sims[i]])
        fhdr = all_authors[sims[i]][0]['name'].split()[-1] + all_arxivid[sims[i]][0:2] +'_'+ all_arxivid[sims[i]]
        fhdrs.append(fhdr)
        textstr = textstr + str(i+1)+'. **'+ all_titles[sims[i]] +'** (Distance: %.2f' %dists[i]+')   \n'
        textstr = textstr + '**ArXiv:** ['+all_arxivid[sims[i]]+'](https://arxiv.org/abs/'+all_arxivid[sims[i]]+')  \n'
        if show_authors == True:
            textstr = textstr + '**Authors:**  '
            temp = all_authors[sims[i]]
            for ak in range(len(temp)):
                if ak < len(temp)-1:
                    textstr = textstr + temp[ak].name + ', '
                else:
                    textstr = textstr + temp[ak].name + '   \n'
        if show_summary == True:
            textstr = textstr + '**Summary:**  '
            text = all_text[sims[i]]
            text = text.replace('\n', ' ')
            textstr = textstr + summarizer.summarize(text) + '  \n'
        if show_authors == True or show_summary == True:
            textstr = textstr + ' '
        textstr = textstr + '  \n'
    return textstr, abstracts_relevant, fhdrs, sims

model_data = [arxiv_ada_embeddings, embeddings, all_titles, all_text, all_authors]

def run_query(query, return_n = 3, yrmin = 1990, yrmax = 2024, show_pure_answer = False, show_all_sources = True):

    show_authors = True
    show_summary = True
    sims, absts, fhdrs, simids = list_similar_papers_v2(model_data,
                                  doc_id = query,
                                  input_type='keywords',
                                  show_authors = show_authors, show_summary = show_summary,
                                  return_n = return_n, yrmin = 1990, yrmax = 2024)

    temp_abst = ''
    loaders = []
    for i in range(len(absts)):
        temp_abst = absts[i]

        try:
            text_file = open("absts/"+fhdrs[i]+".txt", "w")
        except:
            os.mkdir('absts')
            text_file = open("absts/"+fhdrs[i]+".txt", "w")
        n = text_file.write(temp_abst)
        text_file.close()
        loader = TextLoader("absts/"+fhdrs[i]+".txt")
        loaders.append(loader)

    lc_index = VectorstoreIndexCreator().from_loaders(loaders)

    st.markdown('### User query: '+query)
    if show_pure_answer == True:
        st.markdown('pure answer:')
        st.markdown(lc_index.query(query))
        st.markdown(' ')
    st.markdown('#### context-based answer from sources:')
    output = lc_index.query_with_sources(query + ' Let\'s work this out in a step by step way to be sure we have the right answer.' ) #zero-shot in-context prompting from Zhou+22, Kojima+22
    st.markdown(output['answer'])
    opstr = '#### Primary sources: \n'
    st.markdown(opstr)

#     opstr = ''
#     for i in range(len(output['sources'])):
#         opstr = opstr +'\n'+ output['sources'][i]

    textstr = ''
    ng = len(output['sources'].split())
    abs_indices = []

    for i in range(ng):
        if i == (ng-1):
            tempid = output['sources'].split()[i].split('_')[1][0:-4]
        else:
            tempid = output['sources'].split()[i].split('_')[1][0:-5]
        try:
            abs_index = all_arxivid.index(tempid)
            abs_indices.append(abs_index)
            textstr = textstr + str(i+1)+'. **'+ all_titles[abs_index] +'   \n'
            textstr = textstr + '**ArXiv:** ['+all_arxivid[abs_index]+'](https://arxiv.org/abs/'+all_arxivid[abs_index]+')  \n'
            textstr = textstr + '**Authors:**  '
            temp = all_authors[abs_index]
            for ak in range(4):
                if ak < len(temp)-1:
                    textstr = textstr + temp[ak].name + ', '
                else:
                    textstr = textstr + temp[ak].name + '   \n'
            if len(temp) > 3:
                textstr = textstr + ' et al.    \n'
            textstr = textstr + '**Summary:**  '
            text = all_text[abs_index]
            text = text.replace('\n', ' ')
            textstr = textstr + summarizer.summarize(text) + '  \n'
        except:
            textstr = textstr + output['sources'].split()[i]
        #         opstr = opstr + '  \n ' + output['sources'].split()[i][6:-5].split('_')[0]
        #     opstr = opstr + '  \n Arxiv id: ' + output['sources'].split()[i][6:-5].split('_')[1]

        textstr = textstr + ' '
        textstr = textstr + '  \n'
    st.markdown(textstr)

    fig = plt.figure(figsize=(9,9))
    plt.scatter(e2d[0:,0], e2d[0:,1],s=2)
    plt.scatter(e2d[simids,0], e2d[simids,1],s=30)
    plt.scatter(e2d[abs_indices,0], e2d[abs_indices,1],s=100,color='k',marker='d')
    st.pyplot(fig)

    if show_all_sources == True:
        st.markdown('\n #### Other interesting papers:')
        st.markdown(sims)
    return output

st.title('ArXiv-based question answering')
st.markdown('[Includes papers up to: `'+dateval+'`]')
st.markdown('Concise answers for questions using arxiv abstracts + GPT-4. Please use sparingly because it costs me money right now. You might need to wait for a few seconds for the GPT-4 query to return an answer (check top right corner to see if it is still running).')

query = st.text_input('Your question here:', value="What sersic index does a disk galaxy have?")
return_n = st.slider('How many papers should I show?', 1, 20, 10)
yrmin = st.slider('Min year', 1990,2023, 1990)
yrmax = st.slider('Max year', 1990, 2024, 2024)


sims = run_query(query, return_n = return_n, yrmin = yrmin, yrmax = yrmax)