Initial Docker Space

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

LICENSE

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app.py

@@ -0,0 +1,87 @@
+from flask import Flask, render_template, jsonify, request
+from src.helper import download_embeddings
+from langchain_pinecone import PineconeVectorStore
+from langchain_openai import ChatOpenAI
+from langchain.chains import create_retrieval_chain
+from langchain.chains.combine_documents import create_stuff_documents_chain
+from langchain_core.prompts import ChatPromptTemplate
+from langchain.schema import Document
+from dotenv import load_dotenv
+from src.prompt import *
+import os
+from transformers import pipeline
+from langchain_community.llms import HuggingFacePipeline
+
+# Cleaning function for model output
+import re
+
+def clean_text(text):
+    text = re.sub(r'-\n', '', text)
+    text = text.replace('\n', ' ')
+    text = re.sub(r' +', ' ', text)
+    text = re.sub(r'/C\d+', '', text)
+    # Remove lines with 'Reproduced by permission' or 'GALE ENCYCLOPEDIA OF MEDICINE'
+    text = re.sub(r'Reproduced by permission[^\.\n]*[\.]?', '', text, flags=re.IGNORECASE)
+    text = re.sub(r'GALE ENCYCLOPEDIA OF MEDICINE[^\.\n]*[\.]?', '', text, flags=re.IGNORECASE)
+    text = re.sub(r'Researchers,? Inc[^\.\n]*[\.]?', '', text, flags=re.IGNORECASE)
+    return text.strip()
+
+
+app = Flask(__name__)
+
+# Add a greeting document to the Pinecone index
+
+
+
+load_dotenv()
+
+Pinecone_API_KEY = os.getenv("Pinecone_API_KEY")
+os.environ["PINECONE_API_KEY"] = Pinecone_API_KEY
+
+embeddings = download_embeddings()
+
+index_name = "doctor-ai"
+docsearch=PineconeVectorStore.from_existing_index(
+    index_name=index_name,
+    embedding=embeddings
+)
+
+
+retriever= docsearch.as_retriever(search_type="similarity",search_kwargs={"k": 2})
+
+
+generator = pipeline(    "text2text-generation", model="google/flan-t5-large", device=-1)
+chat_model = HuggingFacePipeline(pipeline=generator)
+#prompt= ChatPromptTemplate.from_messages(
+#    [
+#        ("system", system_prompt),
+#        ("human", "{input}")
+#    ]
+#)
+
+
+prompt = ChatPromptTemplate.from_template(system_prompt)
+question_answer_chain = create_stuff_documents_chain(chat_model, prompt)
+rag_chain = create_retrieval_chain(retriever, question_answer_chain)
+
+#question_answer_chain = create_stuff_documents_chain(chat_model, prompt)
+#rag_chain = create_retrieval_chain(retriever, question_answer_chain)
+
+
+@app.route('/')
+def index():
+    return render_template('chat.html')
+
+@app.route('/get', methods=["GET","POST"])
+def chat():
+    msg=request.form["msg"]
+    input=msg
+    print(input)
+    response = rag_chain.invoke({"input": input})
+    cleaned_answer = clean_text(response["answer"])
+    print("Response:", cleaned_answer)
+    return str(cleaned_answer)
+
+
+if __name__ == '__main__':
+    app.run(host='0.0.0.0', port=8000, debug=True)

requirements.txt

@@ -0,0 +1,9 @@
+langchain==0.3.26
+flask==3.1.1
+sentence-transformers==4.1.0
+pypdf==5.6.1
+python-dotenv==1.1.0
+langchain-pinecone==0.2.8
+langchain-openai==0.3.24
+langchain-community==0.3.26
+-e .

setup.py

@@ -0,0 +1,12 @@
+from setuptools import find_packages, setup
+
+setup(
+    name="Medical-Chatbot",
+    version="0.1.0",
+    author="Manail Fatima",
+    author_email="manailfatima2@gmail.com",
+    
+    packages=find_packages(where="src"),
+    package_dir={"": "src"},
+    install_requires=[]
+)

src/helper.py

@@ -0,0 +1,48 @@
+from langchain.document_loaders import PyPDFLoader, DirectoryLoader
+from langchain.text_splitter import RecursiveCharacterTextSplitter
+from typing import List
+from langchain.schema import Document
+from langchain_community.embeddings import HuggingFaceEmbeddings
+
+
+def load_pdf_files(data):
+    loader = DirectoryLoader(
+        data,
+        glob="*.pdf", 
+        loader_cls=PyPDFLoader,
+        show_progress=True
+        )
+    
+    documents = loader.load()
+    return documents
+
+def filter_to_minimal_docs(docs: List[Document]) -> List[Document]:
+    minimal_docs : List[Document]= []
+    for doc in docs:
+        source = doc.metadata.get("source")
+        minimal_docs.append(
+            Document(
+                page_content=doc.page_content,
+                metadata={
+                    "source": source}))
+    return minimal_docs
+
+def text_splitter(minimal_docs):
+    text_splitter = RecursiveCharacterTextSplitter(
+        chunk_size=500,
+        chunk_overlap=20
+        )
+    text_chunks=text_splitter.split_documents(minimal_docs)
+    return text_chunks
+
+def download_embeddings():
+
+    model_name = "sentence-transformers/all-MiniLM-L6-v2"
+    embeddings= HuggingFaceEmbeddings(
+        model_name=model_name,
+       
+    )
+    return embeddings
+embeddings = download_embeddings()
+
+

src/prompt.py

@@ -0,0 +1,9 @@
+system_prompt = (
+    "You are a helpful medical assistant. Use the following context to answer the user's question conversationally. "
+    "If the answer is not in the context, say 'I don't know.' "
+    "Please answer concisely and do not repeat information."
+    "If the user says hi, hello, or hey, reply with 'Hello, I am a helpful medical assistant, how may I help you today?'.\n\n"
+    "Context:\n{context}\n"
+    "Question: {input}\n"
+    "Answer in 2-3 sentences."
+)

static/style.css

@@ -0,0 +1,224 @@
+
+body,html{
+	height: 100%;
+	margin: 0;
+	background: rgb(44, 47, 59);
+   background: -webkit-linear-gradient(to right, rgb(40, 59, 34), rgb(54, 60, 70), rgb(32, 32, 43));
+	background: linear-gradient(to right, rgb(38, 51, 61), rgb(50, 55, 65), rgb(33, 33, 78));
+}
+
+.chat{
+	margin-top: auto;
+	margin-bottom: auto;
+}
+.card{
+	height: 500px;
+	border-radius: 15px !important;
+	background-color: rgba(0,0,0,0.4) !important;
+}
+.contacts_body{
+	padding:  0.75rem 0 !important;
+	overflow-y: auto;
+	white-space: nowrap;
+}
+.msg_card_body{
+	overflow-y: auto;
+}
+.card-header{
+	border-radius: 15px 15px 0 0 !important;
+	border-bottom: 0 !important;
+}
+.card-footer{
+border-radius: 0 0 15px 15px !important;
+	border-top: 0 !important;
+}
+.container{
+	align-content: center;
+}
+.search{
+	border-radius: 15px 0 0 15px !important;
+	background-color: rgba(0,0,0,0.3) !important;
+	border:0 !important;
+	color:white !important;
+}
+.search:focus{
+	 box-shadow:none !important;
+   outline:0px !important;
+}
+.type_msg{
+	background-color: rgba(0,0,0,0.3) !important;
+	border:0 !important;
+	color:white !important;
+	height: 60px !important;
+	overflow-y: auto;
+}
+	.type_msg:focus{
+	 box-shadow:none !important;
+   outline:0px !important;
+}
+.attach_btn{
+	border-radius: 15px 0 0 15px !important;
+	background-color: rgba(0,0,0,0.3) !important;
+	border:0 !important;
+	color: white !important;
+	cursor: pointer;
+}
+.send_btn{
+	border-radius: 0 15px 15px 0 !important;
+	background-color: rgba(0,0,0,0.3) !important;
+	border:0 !important;
+	color: white !important;
+	cursor: pointer;
+}
+.search_btn{
+	border-radius: 0 15px 15px 0 !important;
+	background-color: rgba(0,0,0,0.3) !important;
+	border:0 !important;
+	color: white !important;
+	cursor: pointer;
+}
+.contacts{
+	list-style: none;
+	padding: 0;
+}
+.contacts li{
+	width: 100% !important;
+	padding: 5px 10px;
+	margin-bottom: 15px !important;
+}
+.active{
+	background-color: rgba(0,0,0,0.3);
+}
+.user_img{
+	height: 70px;
+	width: 70px;
+	border:1.5px solid #f5f6fa;
+
+}
+.user_img_msg{
+	height: 40px;
+	width: 40px;
+	border:1.5px solid #f5f6fa;
+
+}
+.img_cont{
+	position: relative;
+	height: 70px;
+	width: 70px;
+}
+.img_cont_msg{
+	height: 40px;
+	width: 40px;
+}
+.online_icon{
+	position: absolute;
+	height: 15px;
+	width:15px;
+	background-color: #4cd137;
+	border-radius: 50%;
+	bottom: 0.2em;
+	right: 0.4em;
+	border:1.5px solid white;
+}
+.offline{
+	background-color: #c23616 !important;
+}
+.user_info{
+	margin-top: auto;
+	margin-bottom: auto;
+	margin-left: 15px;
+}
+.user_info span{
+	font-size: 20px;
+	color: white;
+}
+.user_info p{
+	font-size: 10px;
+	color: rgba(255,255,255,0.6);
+}
+.video_cam{
+	margin-left: 50px;
+	margin-top: 5px;
+}
+.video_cam span{
+	color: white;
+	font-size: 20px;
+	cursor: pointer;
+	margin-right: 20px;
+}
+.msg_cotainer{
+	margin-top: auto;
+	margin-bottom: auto;
+	margin-left: 10px;
+	border-radius: 25px;
+	background-color: rgb(82, 172, 255);
+	padding: 10px;
+	position: relative;
+}
+.msg_cotainer_send{
+	margin-top: auto;
+	margin-bottom: auto;
+	margin-right: 10px;
+	border-radius: 25px;
+	background-color: #58cc71;
+	padding: 10px;
+	position: relative;
+}
+.msg_time{
+	position: absolute;
+	left: 0;
+	bottom: -15px;
+	color: rgba(255,255,255,0.5);
+	font-size: 10px;
+}
+.msg_time_send{
+	position: absolute;
+	right:0;
+	bottom: -15px;
+	color: rgba(255,255,255,0.5);
+	font-size: 10px;
+}
+.msg_head{
+	position: relative;
+}
+#action_menu_btn{
+	position: absolute;
+	right: 10px;
+	top: 10px;
+	color: white;
+	cursor: pointer;
+	font-size: 20px;
+}
+.action_menu{
+	z-index: 1;
+	position: absolute;
+	padding: 15px 0;
+	background-color: rgba(0,0,0,0.5);
+	color: white;
+	border-radius: 15px;
+	top: 30px;
+	right: 15px;
+	display: none;
+}
+.action_menu ul{
+	list-style: none;
+	padding: 0;
+	margin: 0;
+}
+.action_menu ul li{
+	width: 100%;
+	padding: 10px 15px;
+	margin-bottom: 5px;
+}
+.action_menu ul li i{
+	padding-right: 10px;
+}
+.action_menu ul li:hover{
+	cursor: pointer;
+	background-color: rgba(0,0,0,0.2);
+}
+@media(max-width: 576px){
+	.contacts_card{
+	margin-bottom: 15px !important;
+}
+}

store_index.py

@@ -0,0 +1,71 @@
+from langchain_pinecone import PineconeVectorStore
+from datasets import load_dataset
+from langchain.schema import Document
+from src.helper import load_pdf_files, filter_to_minimal_docs, text_splitter, download_embeddings
+from pinecone import Pinecone
+from pinecone import ServerlessSpec
+from dotenv import load_dotenv
+load_dotenv()
+import os
+
+
+Pinecone_API_KEY = os.getenv("Pinecone_API_KEY")
+os.environ["PINECONE_API_KEY"] = Pinecone_API_KEY
+
+
+#extracted_data= load_pdf_files("data")
+#minimal_docs = filter_to_minimal_docs(extracted_data)
+#text_chunks = text_splitter(minimal_docs)
+
+
+embeddings = download_embeddings()
+
+pinecone_API_key=Pinecone_API_KEY
+pc = Pinecone(api_key=pinecone_API_key)
+
+index_name = "doctor-ai"
+if not pc.has_index(index_name):
+    pc.create_index(
+        name=index_name,
+        dimension=384,
+        metric="cosine",
+        spec=ServerlessSpec(
+            cloud="aws",
+            region="us-east-1"
+        ))
+index = pc.Index(index_name) 
+
+
+
+dataset = load_dataset("lavita/ChatDoctor-HealthCareMagic-100k")
+docs = []
+for item in dataset["train"]:
+    question = item.get("instruction", "") + " " + item.get("input", "")
+    answer = item.get("output", "")
+    docs.append(Document(
+        page_content=f"Q: {question}\nA: {answer}",
+        metadata={"source": "huggingface_lavita/ChatDoctor-HealthCareMagic-100k"}
+    ))
+
+
+
+#docssearch=PineconeVectorStore.from_documents(
+#    documents=text_chunks,
+#    embedding=embeddings,
+#    index_name=index_name
+#)
+
+docsearch=PineconeVectorStore.from_existing_index(
+    index_name=index_name,
+    embedding=embeddings
+)
+
+
+def chunked_upload(docs, batch_size=50):
+    for i in range(0, len(docs), batch_size):
+        batch = docs[i:i+batch_size]
+        docsearch.add_documents(batch)
+chunked_upload(docs, batch_size=50)
+
+
+docsearch.add_documents(docs)

template.sh

@@ -0,0 +1,13 @@
+mkdir -p src
+mkdir -p research
+
+touch src/__init.py
+touch src/helper.py
+touch src/prompt.py
+touch .env
+touch setup.py
+touch app.py
+touch research/trials.ipynb
+touch requirements.txt
+
+echo "Created Successfully"

templates/chat.html

@@ -0,0 +1,81 @@
+<link href="//maxcdn.bootstrapcdn.com/bootstrap/4.1.1/css/bootstrap.min.css" rel="stylesheet" id="bootstrap-css">
+<script src="//maxcdn.bootstrapcdn.com/bootstrap/4.1.1/js/bootstrap.min.js"></script>
+<script src="//cdnjs.cloudflare.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
+
+<!DOCTYPE html>
+<html>
+	<head>
+		<title>DoctorAI</title>
+		<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
+		<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.5.0/css/all.css" integrity="sha384-B4dIYHKNBt8Bc12p+WXckhzcICo0wtJAoU8YZTY5qE0Id1GSseTk6S+L3BlXeVIU" crossorigin="anonymous">
+		<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
+		<link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='style.css')}}"/>
+	</head>
+	
+	
+	<body>
+		<div class="container-fluid h-100">
+			<div class="row justify-content-center h-100">		
+				<div class="col-md-8 col-xl-6 chat">
+					<div class="card">
+						<div class="card-header msg_head">
+							<div class="d-flex bd-highlight">
+								<div class="img_cont">
+									<img src="https://cdn-icons-png.flaticon.com/512/387/387569.png" class="rounded-circle user_img">
+									<!-- <img src="https://www.prdistribution.com/spirit/uploads/pressreleases/2019/newsreleases/d83341deb75c4c4f6b113f27b1e42cd8-chatbot-florence-already-helps-thousands-of-patients-to-remember-their-medication.png" class="rounded-circle user_img"> -->
+									<span class="online_icon"></span>
+								</div>
+								<div class="user_info">
+									<span>DoctorAI</span>
+									<p>Ask me anything!</p>
+								</div>
+							</div>
+						</div>
+						<div id="messageFormeight" class="card-body msg_card_body">
+							
+							
+						</div>
+						<div class="card-footer">
+							<form id="messageArea" class="input-group">
+                                <input type="text" id="text" name="msg" placeholder="Type your message..." autocomplete="off" class="form-control type_msg" required/>
+								<div class="input-group-append">
+									<button type="submit" id="send" class="input-group-text send_btn"><i class="fas fa-location-arrow"></i></button>
+								</div>
+							</form>
+						</div>
+					</div>
+				</div>
+			</div>
+		</div>
+		
+		<script>
+			$(document).ready(function() {
+				$("#messageArea").on("submit", function(event) {
+					const date = new Date();
+					const hour = date.getHours();
+					const minute = date.getMinutes();
+					const str_time = hour+":"+minute;
+					var rawText = $("#text").val();
+
+					var userHtml = '<div class="d-flex justify-content-end mb-4"><div class="msg_cotainer_send">' + rawText + '<span class="msg_time_send">'+ str_time + '</span></div><div class="img_cont_msg"><img src="https://i.ibb.co/d5b84Xw/Untitled-design.png" class="rounded-circle user_img_msg"></div></div>';
+					
+					$("#text").val("");
+					$("#messageFormeight").append(userHtml);
+
+					$.ajax({
+						data: {
+							msg: rawText,	
+						},
+						type: "POST",
+						url: "/get",
+					}).done(function(data) {
+						var botHtml = '<div class="d-flex justify-content-start mb-4"><div class="img_cont_msg"><img src="https://cdn-icons-png.flaticon.com/512/387/387569.png" class="rounded-circle user_img_msg"></div><div class="msg_cotainer">' + data + '<span class="msg_time">' + str_time + '</span></div></div>';
+						$("#messageFormeight").append($.parseHTML(botHtml));
+					});
+					event.preventDefault();
+				});
+			});
+		</script>
+        
+    </body>
+</html>