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app.py

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+import os
+import requests
+from io import BytesIO
+from PyPDF2 import PdfReader
+import pandas as pd
+from openai.embeddings_utils import get_embedding, cosine_similarity
+import openai
+import streamlit as st
+import numpy as np
+import base64
+import faiss
+
+
+
+messages = [
+    {"role": "system", "content": "You are SummarizeGPT, a large language model whose expertise is reading and summarizing scientific papers."}
+]
+
+class Chatbot():
+    
+    def parse_paper(self, pdf):
+        # This function parses the PDF and returns a list of dictionaries with the text, 
+        # font size, and x and y coordinates of each text element in the PDF
+        print("Parsing paper")
+        number_of_pages = len(pdf.pages)
+        print(f"Total number of pages: {number_of_pages}")
+        # This is the list that will contain all the text elements in the PDF and will be returned by the function
+        paper_text = []
+        
+        for i in range(number_of_pages):
+            # Iterate through each page in the PDF, and extract the text elements. pdf.pages is a list of Page objects.
+            page = pdf.pages[i]
+            # This is the list that will contain all the text elements in the current page
+            page_text = []
+
+            def visitor_body(text, cm, tm, fontDict, fontSize):
+                # tm is a 6-element tuple of floats that represent a 2x3 matrix, which is the text matrix for the text.
+                # The first two elements are the horizontal and vertical scaling factors, the third and fourth elements 
+                # are the horizontal and vertical shear factors, and the fifth and sixth elements are the horizontal and vertical translation factors.
+                
+                # x and y are the coordinates of the text element
+                x = tm[4]
+                y = tm[5]
+                
+                # ignore header/footer, and empty text.
+                # The y coordinate is used to filter out the header and footer of the paper
+                # The length of the text is used to filter out empty text
+                if (y > 50 and y < 720) and (len(text.strip()) > 1):
+                    page_text.append({
+                    # The fontsize is used to separate paragraphs into different elements in the paper_text list
+                    'fontsize': fontSize,
+                    # The text is stripped of whitespace and the \x03 character
+                    'text': text.strip().replace('\x03', ''),
+                    # The x and y coordinates are used to separate paragraphs into different elements in the paper_text list
+                    'x': x,
+                    'y': y
+                    })
+
+            # Extract the text elements from the page
+            _ = page.extract_text(visitor_text=visitor_body)
+            print(f'Page {i} text", {page_text}')
+
+            
+            blob_font_size = None
+            blob_text = ''
+            processed_text = []
+
+            for t in page_text:
+                if t['fontsize'] == blob_font_size:
+                    blob_text += f" {t['text']}"
+                    if len(blob_text) >= 2000:
+                        processed_text.append({
+                            'fontsize': blob_font_size,
+                            'text': blob_text,
+                            'page': i
+                        })
+                        blob_font_size = None
+                        blob_text = ''
+                else:
+                    if blob_font_size is not None and len(blob_text) >= 1:
+                        processed_text.append({
+                            'fontsize': blob_font_size,
+                            'text': blob_text,
+                            'page': i
+                        })
+                    blob_font_size = t['fontsize']
+                    blob_text = t['text']
+                paper_text += processed_text
+        print("Done parsing paper")
+        print(paper_text)
+
+        return paper_text
+
+    def paper_df(self, pdf):
+        print('Creating dataframe')
+        filtered_pdf= []
+        for row in pdf:
+            # This will use the get method to safely access the 'text' key in the row dictionary, 
+            # and if the key is not present, it will use an empty string as a default value. This 
+            # should prevent a KeyError from occurring.
+            if len(row.get('text', '')) < 30:
+                continue
+            filtered_pdf.append(row)
+        print("Filtered paper_text", filtered_pdf)
+        df = pd.DataFrame(filtered_pdf)
+        print(df.shape)
+        print(df.head)
+        # remove elements with identical df[text] and df[page] values
+        df = df.drop_duplicates(subset=['text', 'page'], keep='first')
+        df['length'] = df['text'].apply(lambda x: len(x))
+        print('Done creating dataframe')
+        return df
+
+    def calculate_embeddings(self, df):
+        print('Calculating embeddings')
+        openai.api_key = os.getenv('OPENAI_API_KEY')
+        embedding_model = "text-embedding-ada-002"
+        # Get the embeddings for each text element in the dataframe
+        embeddings = df.text.apply(lambda x: get_embedding(x, engine=embedding_model))
+        embeddings = np.vstack(embeddings, dtype=np.float32)
+        return embeddings    
+
+    def search_embeddings(self, embeddings, df, query, n=3, pprint=True):
+        
+        # Step 1. Get an embedding for the question being asked to the PDF
+        query_embedding = get_embedding(query, engine="text-embedding-ada-002")
+        query_embedding = np.array(query_embedding, dtype=np.float32)
+        # Step 2. Create a FAISS index and add the embeddings
+        d = embeddings.shape[1]
+        # Use the L2 distance metric
+        index = faiss.IndexFlatL2(d)
+        print("Embeddings shape:", embeddings.shape)
+        print("Embeddings data type:", type(embeddings))
+        index.add(embeddings)
+        
+        
+        # Step 3. Search the index for the embedding of the question
+
+        D, I = index.search(query_embedding.reshape(1,d), n)        
+        
+        # Step 4. Get the top n results from the dataframe
+        results = df.iloc[I[0]]
+        results['similarity'] = D[0]
+        results = results.reset_index(drop=True)
+        
+        # Make a dictionary of the first n results with the page number as the key and the text as the value
+        
+        global sources 
+        sources = []
+        for i in range(n):
+            # append the page number and the text as a dict to the sources list
+            sources.append({'Page '+str(results.iloc[i]['page']): results.iloc[i]['text'][:150]+'...'})
+        print(sources)
+        return results.head(n)
+    
+    def create_prompt(self, embeddings, df, user_input):
+        result = self.search_embeddings(embeddings, df, user_input, n=3)
+        print(result)
+        prompt = """
+        You are Research Paper Guru
+        The user is going to ask you a question about a research paper after uploading a PDF of the paper.
+        You are a large language model whose expertise is reading and and providing answers to their queries, based on what you know about the subject as well as what you know about the text given to you.
+            
+            The user asks: """+ user_input + """
+            
+            And the information about the paper that is relevant to the question is: 
+            
+            1.""" + str(result.iloc[0]['text']) + """
+            2.""" + str(result.iloc[1]['text']) + """
+            3.""" + str(result.iloc[2]['text']) + """
+
+            Knowing what you know about this answer, as well as being able to navigate this knowledge in conjuction with what is being said in the paper, provide an answer to the user. If the person asks you to summarize what is in the paper, do your best to provide a summary of the paper.
+            The goal here is to keep the user happy and satisfied that you have given them the best answer to the question to the best of your knowledge. If necessary, you can also point them to outside resources for more information.:"""
+
+        print('Done creating prompt')
+        return prompt
+
+    def gpt(self, prompt):
+        openai.api_key = os.getenv('OPENAI_API_KEY')
+        print('got API key')
+        messages.append({"role": "user", "content": prompt})
+        r = openai.ChatCompletion.create(model="gpt-3.5-turbo", messages=messages)
+        answer = r['choices'][0]['message']['content']
+        response = {'answer': answer, 'sources': sources}
+        return response
+
+    def reply(self, embeddings, user_input):
+        print(user_input)
+        prompt = self.create_prompt(embeddings, df, user_input)
+        return self.gpt(prompt)
+
+def process_pdf(file):
+    print("Processing pdf")
+    pdf = PdfReader(BytesIO(file))
+    chatbot = Chatbot()
+    paper_text = chatbot.parse_paper(pdf)
+    global df
+    df = chatbot.paper_df(paper_text)
+    embeddings = chatbot.calculate_embeddings(df)
+    print("Done processing pdf")
+    return embeddings
+
+def download_pdf(url):
+    chatbot = Chatbot()
+    r = requests.get(str(url))
+    print(r.headers)
+    pdf = PdfReader(BytesIO(r.content))
+    paper_text = chatbot.parse_paper(pdf)
+    global df
+    df = chatbot.paper_df(paper_text)
+    embeddings = chatbot.calculate_embeddings(df)
+    print("Done processing pdf")
+    return embeddings
+
+def show_pdf(file_content):
+    base64_pdf = base64.b64encode(file_content).decode('utf-8')
+    pdf_display = f'<iframe src="data:application/pdf;base64,{base64_pdf}" width="800" height="800" type="application/pdf"></iframe>'
+    st.markdown(pdf_display, unsafe_allow_html=True)
+
+
+def main():
+    st.title("Research Paper Guru")
+    st.subheader("Upload PDF or Enter URL")
+    embeddings = None
+    pdf_option = st.selectbox("Choose an option:", ["Upload PDF", "Enter URL"])
+    chatbot = Chatbot()
+
+    if pdf_option == "Upload PDF":
+        uploaded_file = st.file_uploader("Choose a PDF file", type="pdf")
+        if uploaded_file is not None:
+            file_content = uploaded_file.read()
+            embeddings = process_pdf(file_content)
+            st.success("PDF uploaded and processed successfully!")
+            show_pdf(file_content)
+
+    elif pdf_option == "Enter URL":
+        url = st.text_input("Enter the URL of the PDF:")
+        if url:
+            if st.button("Download and process PDF"):
+                try:
+                    r = requests.get(str(url))
+                    content = r.content
+                    embeddings = download_pdf(url)
+                    st.success("PDF downloaded and processed successfully!")
+                    show_pdf(content)
+                except Exception as e:
+                    st.error(f"An error occurred while processing the PDF: {e}")
+    st.subheader("Ask a question about a research paper and get an answer with sources!")
+    query = st.text_input("Enter your query:")
+    if query:
+        if st.button("Get answer"):
+            if embeddings is not None:
+                response = chatbot.reply(embeddings, query)
+            else:
+                st.warning("Please upload a PDF or enter a URL first.")
+            st.write(response['answer'])
+            st.write("Sources:")
+            for source in response['sources']:
+                st.write(source)
+
+if __name__ == "__main__":
+    main()
+    

requirements.txt

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+flask
+PyPDF2
+pandas
+openai==0.27.2
+requests
+flask-cors
+matplotlib
+scipy
+plotly
+google-cloud-storage
+gunicorn==20.1.0
+scikit-learn
+faiss-cpu
+altair<5