✨Entity Linking Application✨.py

import json
import numpy as np
import re
from itertools import combinations as itertools_combinations
import os
import sys
from SPARQLWrapper import SPARQLWrapper, JSON
from sentence_transformers import SentenceTransformer
import aiohttp
import asyncio
import streamlit as st
import time
from openai import OpenAI
import sys
import time
from bs4 import BeautifulSoup
import requests
import nest_asyncio
import httpx


nest_asyncio.apply()


folder_path = '/home/user/app/qids_folder'

if not os.path.exists(folder_path):
    os.mkdir(folder_path)
else:
    pass


folder_path_1 = '/home/user/app/info_extraction'

if not os.path.exists(folder_path_1):
    os.mkdir(folder_path_1)
    print(f"Folder created at {folder_path_1}")
else:
    pass

model = SentenceTransformer("Lajavaness/bilingual-embedding-large", trust_remote_code=True)

async def fetch_json(url, session):
    async with session.get(url) as response:
        return await response.json()

async def combination_method(name, session):
    async with aiohttp.ClientSession() as session:
        data = set()
        new_name = name.split()
        x = itertools_combinations(new_name, 2)
        for i in x:
            new_word = (i[0] + " " + i[1])
            url = f"https://en.wikipedia.org/w/api.php?action=query&list=search&srsearch={new_word}&srlimit=20&srprop=&srenablerewrites=True&format=json"
            json_data = await fetch_json(url, session)
            suggestion = json_data.get('query', {}).get('search', {})
            for pageid in suggestion:
                data.add(pageid.get('title', {}))
    return data

async def single_method(name, session):
    async with aiohttp.ClientSession() as session:
        data = set()
        new_name = name.replace("-", " ").replace("/", " ").split()
        for i in new_name:
            url = f"https://en.wikipedia.org/w/api.php?action=query&list=search&srsearch={i}&srlimit=20&srprop=&srenablerewrites=True&format=json"
            json_data = await fetch_json(url, session)
            suggestion = json_data.get('query', {}).get('search', {})
            for pageid in suggestion:
                data.add(pageid.get('title', {}))
    return data

async def mains(name, deep_search):
    data = set()
    disam_data = set()
    qids = set()
    
    async with aiohttp.ClientSession() as session:
        url = f"https://en.wikipedia.org/w/api.php?action=query&list=search&srsearch={name}&srlimit=20&srprop=&srenablerewrites=True&format=json"
        json_data = await fetch_json(url, session)
        suggestion = json_data.get('query', {}).get('search', {})
        for pageid in suggestion:
            data.add(pageid.get('title', {}))

        wikipedia_url = f"https://en.wikipedia.org/w/api.php?action=query&list=search&srsearch={name}&srlimit=1&srprop=&srenablerewrites=True&srinfo=suggestion&format=json"
        json_data = await fetch_json(wikipedia_url, session)
        suggestion = json_data.get('query', {}).get('searchinfo', {}).get('suggestion')

        if suggestion:
            suggested_url = f"https://en.wikipedia.org/w/api.php?action=query&list=search&srsearch={suggestion}&srlimit=10&srprop=&srenablerewrites=True&srinfo=suggestion&format=json"
            json_suggestion = await fetch_json(suggested_url, session)
            results = json_suggestion.get('query', {}).get('search')
            for i in results:
                    data.add(i.get('title'))

        # Handle disambiguation links
        if data != {0}:
            for ids in data:
                titles = set()
                wikipedia_disambiguation = f"https://en.wikipedia.org/w/api.php?action=query&generator=links&format=json&redirects=1&pageids={ids}&prop=pageprops&gpllimit=50&ppprop=wikibase_item"
                json_id = await fetch_json(wikipedia_disambiguation, session)
                try:
                    title = json_id.get('query').get('pages')
                    for k, v in title.items():
                        titles.add(v.get("title"))
                except:
                    pass

                if "Help:Disambiguation" in titles:
                    for i in titles:
                        if ":" not in i:
                            disam_data.add(i)
                else:
                    disam_data.add(ids)

        # Makes combinations of the name
        if deep_search == "Yes":
            if len(name.replace("-", " ").split()) >= 3: 
                combination_names = await combination_method(name, session)
                for i in combination_names:
                    disam_data.add(i)

        # Checks every word alone
        if deep_search == "Yes":
            if len(name.replace("-", " ").replace("/", " ").split()) >= 2:
                singles = await single_method(name, session)
                for i in singles:
                    disam_data.add(i)

        for ids in disam_data:
            try:
                wikibase_url = f"https://en.wikipedia.org/w/api.php?action=query&titles={ids}&prop=pageprops&format=json"
                json_qid = await fetch_json(wikibase_url, session)
                wikidata_qid = json_qid.get('query', {}).get('pages', {})
                for page_id, page_data in wikidata_qid.items():
                    page_props = page_data.get('pageprops', {})
                    wikibase_item = page_props.get('wikibase_item', None)
                    if wikibase_item:
                        qids.add(wikibase_item)
            except:
                pass

        with open(f"/home/user/app/qids_folder/{name}.json", "w") as f:
            json.dump(list(qids), f)


async def get_results(query):
    user_agent = "WDQS-example Python/%s.%s" % (sys.version_info[0], sys.version_info[1])
    url = "https://query.wikidata.org/sparql"
    sparql = SPARQLWrapper(url, agent=user_agent)
    sparql.setQuery(query)
    sparql.setReturnFormat(JSON)
    return sparql.query().convert()
    
def get_resultss(query):
    user_agent = "WDQS-example Python/%s.%s" % (sys.version_info[0], sys.version_info[1])
    url = "https://query.wikidata.org/sparql"
    sparql = SPARQLWrapper(url, agent=user_agent)
    sparql.setQuery(query)
    sparql.setReturnFormat(JSON)
    return sparql.query().convert()

    
def cleaner(text):
    text = text.replace('\\', '').replace('\n', ' ')
    text = re.sub(r'\{.*?\}', '', text)
    text = re.sub(' +', ' ', text).strip()
    return text

async def retriever(qid):
    async with aiohttp.ClientSession() as session: 
        list_with_sent = []

        query_label = f"""SELECT ?subjectLabel
          WHERE {{
            wd:{qid} rdfs:label ?subjectLabel .
            FILTER(LANG(?subjectLabel) = "en")
          }}
          """

        results = await get_results(query_label)

        label = None
        if results["results"]["bindings"]:
            for result in results["results"]["bindings"]:
                for key, value in result.items():
                    label = value.get("value", {}).lower()

        query_alias = f"""SELECT ?alias
          WHERE {{
            wd:{qid} skos:altLabel ?alias
            FILTER(LANG(?alias) = "en")
          }}
          """

        alias_list = []
        results = await get_results(query_alias)

        for result in results["results"]["bindings"]:
            for key, value in result.items():
                alias = value.get("value", "None")
                alias_list.append(alias)

        query_desci = f"""SELECT ?subjectLabel
        WHERE {{
        ?subjectLabel schema:about wd:{qid} ;
                      schema:inLanguage "en" ;
                      schema:isPartOf <https://en.wikipedia.org/> .
        }}
        """

        results = await get_results(query_desci)
        cleaned_first_para = "None"
        
        if results["results"]["bindings"]:
            for result in results["results"]["bindings"]:
                for key, value in result.items():
                    desc = value.get("value", "None")

                title = desc.split("/wiki/")[1]

                url = f"https://en.wikipedia.org/w/api.php?action=query&prop=extracts&titles={title}&exintro=&exsentences=2&explaintext=&redirects=&formatversion=2&format=json"
                
     
                json_data = await fetch_json(url, session)
                cleaned_first_para = cleaner(json_data.get('query', {}).get('pages', [{}])[0].get('extract', 'None'))
        else:
            query_desc = f"""SELECT ?subjectLabel
            WHERE {{
            wd:{qid} schema:description ?subjectLabel .
            FILTER(LANG(?subjectLabel) = "en")
            }}
            """

            results = await get_results(query_desc)
            if results["results"]["bindings"]:
                for result in results["results"]["bindings"]:
                    for key, value in result.items():
                        cleaned_first_para = value.get("value", "None")

        list_with_sent.append({"qid": qid, "label": label, "description": cleaned_first_para})

        if alias_list:
            for alias in alias_list:
                list_with_sent.append({"qid": qid, "label": alias.lower(), "description": cleaned_first_para})

        return list_with_sent

async def main(name):
    with open(f"/home/user/app/qids_folder/{name}.json", "r") as f:
        final_list = []
        qids = json.load(f)
        for q in qids:
            returned_list = await retriever(q)
            if returned_list:
                final_list.extend(returned_list)

        with open(f"/home/user/app/info_extraction/{name}.json", "w", encoding="utf-8") as flast:
            json.dump(final_list, flast)

def main_cli():
    st.title("✨ Entity Linking Application ✨")
    st.caption("This web application is part of my master’s dissertation.")

    if 'run_button' in st.session_state and st.session_state.run_button == True:
        st.session_state.running = True
    else:
        st.session_state.running = False
        
    api_token = st.text_input("Enter your API key from [GitHub](https://github.com/marketplace/models/azure-openai/gpt-4o):", "", type="password", disabled=st.session_state.running)   
    
    if api_token:
        endpoint = "https://models.inference.ai.azure.com"
        model_name = "gpt-4o"
        client = OpenAI(
        base_url=endpoint,
        api_key=api_token,
    )
        st.success("API Token is set for this session.")
    else:
        st.warning("Please enter an API token to proceed.")
        
    input_sentence_user = st.text_input("Enter a sentence:", "", disabled=st.session_state.running)
    input_mention_user = st.text_input("Enter a textural reference (mention) that is inside the sentence:", "", disabled=st.session_state.running)
    deep_search = st.selectbox("Perform deep search? (Useful for difficult mentions)", ['Yes', 'No'], index=1, disabled=st.session_state.running)
    disambi = st.selectbox("Run acronym disambiguation? (Enable it if the mention include an acronym or if it is nested)", ['Yes', 'No'], index=0, disabled=st.session_state.running)
    
    if st.button("Run Entity Linking", key="run_button", disabled=st.session_state.running):
        if input_sentence_user and input_mention_user:
            # check if the mention is in the sentence
            if input_mention_user in input_sentence_user:
                with st.spinner("Applying Data Normalization module... (1/5)"):
                # Data Normalization               
                    start_time = time.time()
                    
                    list_with_full_names = []
                    list_with_names_to_show = []
                     
                    if disambi == "Yes":
                        response = client.chat.completions.create(
                            messages=[
                                {
                                    "role": "system",
                                    "content": """
                                                I will give you one or more labels within a sentence. Your task is as follows:
    
                                                Identify each label in the sentence, and check if it is an acronym.
    
                                                If the label is an acronym, respond with the full name of the acronym.
                                                If the label is not an acronym, respond with the label exactly as it was given to you.
                                                If a label contains multiple terms (e.g., 'phase and DIC microscopy'), treat each term within the label as a separate label.
    
                                                This means you should identify and explain each part of the label individually.
                                                Each part should be on its own line in the response.
                                                Context-Specific Terms: If the sentence context suggests a relevant term that applies to each label (such as "study" in 'morphological, sedimentological, and stratigraphical study'), add that term to each label’s explanation.
    
                                                Use context clues to determine the appropriate term to add (e.g., 'study' or 'microscopy').
                                                Output Format: Your response should contain only the explanations, formatted as follows:
    
                                                Each label or part of a label should be on a new line.
                                                Do not include any additional text, and do not repeat the original sentence.
                                                Example 1:
    
                                                Input:
    
                                                label: phase and DIC microscopy
                                                context: Tardigrades have been extracted from samples using centrifugation with Ludox AM™ and mounted on individual microscope slides in Hoyer's medium for identification under phase and DIC microscopy.
                                                Expected response:
    
                                                phase: phase microscopy
                                                DIC microscopy: Differential interference contrast microscopy
                                                Example 2:
    
                                                Input:
    
                                                label: morphological, sedimentological, and stratigraphical study
                                                context: This paper presents results of a morphological, sedimentological, and stratigraphical study of relict beach ridges formed on a prograded coastal barrier in Bream Bay, North Island New Zealand.
                                                Expected response:
    
                                                morphological: morphological study
                                                sedimentological: sedimentological study
                                                stratigraphical: stratigraphical study
                                                IMPORTANT:
    
                                                Each label, even if nested within another, should be treated as an individual item.
                                                Each individual label or acronym should be output on a separate line.                               
                                                """
                                },
                                {
                                    "role": "user",
                                    "content": f"label:{input_mention_user}, context:{input_sentence_user}"
                                }
                            ],
                            temperature=1.0,
                            top_p=1.0,
                            max_tokens=1000,
                            model=model_name
                        )
                       
                        
                        kati = response.choices[0].message.content.splitlines()
                        print(response.choices[0].message.content)
                        for i in kati:
                            context = i.split(":")[-1].strip()
                            original_name = i.split(":")[0].strip()
                            list_with_full_names.append(context)
                            list_with_names_to_show.append(original_name)
                            
                        name = ",".join(list_with_full_names)
    
                    else:
                        name = input_mention_user
                        list_with_full_names.append(name)
                        list_with_names_to_show.append(name)
                    
                    input_sentence_user = input_sentence_user.replace(input_mention_user, name)  # Changing the mention to the correct one
                    
                    response = client.chat.completions.create(
                            messages=[
                                {
                                    "role": "system",
                                    "content": "Given a label or labels within a sentence, provide a brief description (2-3 sentences) explaining what the label represents, similar to how a Wikipedia entry would. Format your response as follows: label: description. I want only the description of the label, not the role in the context. Include the label in the description as well. For example: Sentiment analysis: Sentiment analysis is the use of natural language processing, text analysis, computational linguistics, and biometrics to systematically identify, extract, quantify, and study affective states and subjective information.\nText analysis: Text mining, text data mining (TDM) or text analytics is the process of deriving high-quality information from text. It involves the discovery by computer of new, previously unknown information, by automatically extracting information from different written resources.",
                                },
                                {
                                    "role": "user",
                                    "content": f"label:{name}, context:{input_sentence_user}"
                                }
                            ],
                            temperature=1.0,
                            top_p=1.0,
                            max_tokens=1000,
                            model=model_name
                        )
    
                    
                    z = response.choices[0].message.content.splitlines()
                    print(response.choices[0].message.content)
                    list_with_contexts = []
                    for i in z:
                        context = i.split(":")[-1].strip()
                        list_with_contexts.append(context)
                st.write("✅ Applied Data Normilzation module (1/5)")
                # Candidate Retrieval & Information Gathering
                async def big_main(mention, deep_search):
                    mention = mention.split(",")
                    with st.spinner("Applying Candidate Retrieval module... (2/5)"):
                        for i in mention:
                            await mains(i, deep_search)
                    st.write("✅ Applied Candidate Retrieval module (2/5)")
                    with st.spinner("Applying Information Gathering module... (3/5)"):
                        for i in mention:
                            await main(i)
                    st.write("✅ Applied Information Gathering module (3/5)")
                        
                asyncio.run(big_main(name, deep_search))

                number = 0
                for i,j,o in zip(list_with_full_names,list_with_contexts,list_with_names_to_show):
                    number += 1
                    with st.spinner(f"Applying Candidate Selection module... (4/5) [{number}/{len(list_with_full_names)}] (This may take a while)"):
                        with open(f"/home/user/app/info_extraction/{i}.json", "r") as f:
                            json_file = json.load(f)
                            lista = []
                            lista_1 = []
                            my_bar = st.progress(0)
                            for index, element in enumerate(json_file):
                                qid = element.get("qid")
                                link = f"https://www.wikidata.org/wiki/{qid}"
                                label = element.get("label")
                                description = element.get("description")
                                
                                label_emb = model.encode([label])
                                desc_emb = model.encode([description])
                                
                                lista.append({link: [label_emb, desc_emb]})
                                my_bar.progress((index + 1) / len(json_file))
                                print(qid)
    
                            label_dataset_emb = model.encode([i])
                            desc_dataset_emb = model.encode([j])
    
                            for emb in lista:
                                for k, v in emb.items():
                                    cossim_label = model.similarity(label_dataset_emb, v[0][0])
                                    desc_label = model.similarity(desc_dataset_emb, v[1][0])
                                    emb_mean = np.mean([cossim_label, desc_label])
                                    lista_1.append({k: emb_mean})
    
                            sorted_data = sorted(lista_1, key=lambda x: list(x.values())[0], reverse=True)
                            
                        my_bar.empty()
                        st.write(f"✅ Applined Candidate Selection module (4/5) [{number}/{len(list_with_full_names)}]")
                    with st.spinner(f"Applying Candidate Matching module... (5/5) [{number}/{len(list_with_full_names)}]"):
                        if sorted_data:
                            sorted_top = sorted_data[0]
                            for k, v in sorted_top.items():
                                qid = k.split("/")[-1]
                                
                                wikidata2wikipedia = f"""
                                    SELECT ?wikipedia
                                    WHERE {{
                                          ?wikipedia schema:about wd:{qid} .
                                          ?wikipedia schema:isPartOf <https://en.wikipedia.org/> .
                                    }}
                                    """
                                results = get_resultss(wikidata2wikipedia)

                                for result in results["results"]["bindings"]:
                                    for key, value in result.items():
                                        wikipedia = value.get("value", "None")
                                
                                sparql = SPARQLWrapper("http://dbpedia.org/sparql")
                                wikidata2dbpedia = f"""
                                    SELECT ?dbpedia
                                    WHERE {{
                                          ?dbpedia owl:sameAs <http://www.wikidata.org/entity/{qid}>.
                                    }}
                                    """
                                sparql.setQuery(wikidata2dbpedia)
                                sparql.setReturnFormat(JSON)
                                results = sparql.query().convert()
                                
                                for result in results["results"]["bindings"]:
                                    dbpedia = result["dbpedia"]["value"]
                                    
                                st.write(f"✅ Applied Candidate Matching module (5/5) [{number}/{len(list_with_full_names)}]")    
                                st.text(f"The correct entity for '{o}' is:")    
                                st.success(f"Wikipedia: {wikipedia}")
                                st.success(f"Wikidata: {k}")
                                st.success(f"DBpedia: {dbpedia}")
                        else:
                            st.warning(f"The entity: {o} is NIL.")
            else:
                st.warning(f"The mention '{input_mention_user}' was NOT found in the sentence.")
        else:
            st.warning("Please fill in both fields.")
        end_time = time.time()
        execution_time = end_time - start_time
        ETA = time.strftime("%H:%M:%S", time.gmtime(execution_time))
        st.write(f"⌛ Execution time: {ETA}")
        
        st.button("Rerun", disabled=False)

        # i think this part can be removed now
        folder_path = "qids_folder"
        for filename in os.listdir(folder_path):
            file_path = os.path.join(folder_path, filename)
            os.remove(file_path)
            
        folder_path_1 = "info_extraction"
        for filename in os.listdir(folder_path_1):
            file_path = os.path.join(folder_path_1, filename)
            os.remove(file_path)
            
if __name__ == "__main__":
    main_cli()