Dockerize app and add aws infrastructure

.dockerignore

@@ -0,0 +1,13 @@
+**/.git
+**/.gitignore
+**/.vscode
+**/coverage
+**/.aws
+**/.ssh
+**/.terraform
+Dockerfile
+README.md
+docker-compose.yml
+**/.DS_Store
+**/venv
+**/env

.gitignore

@@ -173,5 +173,7 @@ poetry.toml
 pyrightconfig.json
 
 # data
-# data/
+data/
 study_export_*
+study_files.db
+study_files.json

Dockerfile.api

@@ -0,0 +1,19 @@
+# FastAPI Dockerfile
+FROM python:3.11.10-slim
+
+ENV PYTHONUNBUFFERED=1
+ENV OMP_NUM_THREADS=1
+
+# Set working directory
+WORKDIR /app
+
+# Copy app files
+COPY requirements.txt ./
+RUN pip install --no-cache-dir -r requirements.txt
+COPY . .
+
+# Expose port
+EXPOSE 8000
+
+# Command to run the FastAPI app
+CMD ["uvicorn", "api:app", "--host", "0.0.0.0", "--port", "8000"]

Dockerfile.api.prod

@@ -0,0 +1,68 @@
+###########
+# BUILDER #
+###########
+
+# pull official base image
+FROM 224427659724.dkr.ecr.us-east-1.amazonaws.com/gradio-python:3.11.10-slim as builder
+
+# set work directory
+WORKDIR /app
+
+# set environment variables
+ENV PYTHONDONTWRITEBYTECODE 1
+ENV PYTHONUNBUFFERED 1
+ENV OMP_NUM_THREADS=1
+
+
+# install dependencies
+RUN apt-get update \
+    && apt-get -y install libpq-dev gcc \
+    && pip install psycopg
+
+RUN pip install --upgrade pip
+COPY ./requirements.txt /app/requirements.txt
+RUN pip wheel --no-cache-dir --no-deps --wheel-dir /app/wheels -r requirements.txt
+
+#########
+# FINAL #
+#########
+
+# pull official base image
+FROM 224427659724.dkr.ecr.us-east-1.amazonaws.com/gradio-python:3.11.10-slim
+
+# create directory for the app user
+RUN mkdir -p /home/backend-app
+
+# create the app user
+RUN addgroup --system app && adduser --system --group app
+
+# create the appropriate directories
+ENV HOME=/home/app
+ENV BACKEND_APP_HOME=/home/app
+# RUN mkdir $BACKEND_APP_HOME
+WORKDIR $BACKEND_APP_HOME
+
+# install dependencies
+RUN apt-get update \
+    && apt-get -y install libpq-dev gcc \
+    && pip install psycopg
+
+COPY --from=builder /app/wheels /wheels
+COPY --from=builder /app/requirements.txt .
+RUN pip install --upgrade pip
+RUN pip install --no-cache /wheels/*
+
+# copy project
+COPY . $BACKEND_APP_HOME
+
+# chown all the files to the app user
+RUN chown -R app:app $BACKEND_APP_HOME
+
+# change to the app user
+USER app
+
+## Expose port
+EXPOSE 8000
+
+# Command to run the FastAPI app
+CMD ["uvicorn", "api:app", "--host", "0.0.0.0", "--port", "8000"]

Dockerfile.gradio

@@ -0,0 +1,21 @@
+# Gradio Dockerfile
+FROM python:3.11.10-slim
+
+ENV PYTHONUNBUFFERED=1
+ENV OMP_NUM_THREADS=1
+
+# Set working directory
+WORKDIR /app
+
+# Copy app files
+COPY requirements.txt ./
+RUN pip install --no-cache-dir -r requirements.txt
+COPY . .
+
+# Expose port
+EXPOSE 7860
+ENV GRADIO_SERVER_NAME="0.0.0.0"
+
+# Command to run the Gradio app
+CMD ["gradio", "app.py"]
+# CMD ["python", "app.py"]

Dockerfile.gradio.prod

@@ -0,0 +1,68 @@
+###########
+# BUILDER #
+###########
+
+# pull official base image
+FROM 224427659724.dkr.ecr.us-east-1.amazonaws.com/gradio-python:3.11.10-slim as builder
+
+# set work directory
+WORKDIR /app
+
+# set environment variables
+ENV PYTHONDONTWRITEBYTECODE 1
+ENV PYTHONUNBUFFERED 1
+ENV OMP_NUM_THREADS=1
+
+
+# install dependencies
+RUN apt-get update \
+    && apt-get -y install libpq-dev gcc \
+    && pip install psycopg
+
+RUN pip install --upgrade pip
+COPY ./requirements.txt /app/requirements.txt
+RUN pip wheel --no-cache-dir --no-deps --wheel-dir /app/wheels -r requirements.txt
+
+#########
+# FINAL #
+#########
+
+# pull official base image
+FROM 224427659724.dkr.ecr.us-east-1.amazonaws.com/gradio-python:3.11.10-slim
+
+# create directory for the app user
+RUN mkdir -p /home/backend-app
+
+# create the app user
+RUN addgroup --system app && adduser --system --group app
+
+# create the appropriate directories
+ENV HOME=/home/app
+ENV BACKEND_APP_HOME=/home/app
+# RUN mkdir $BACKEND_APP_HOME
+WORKDIR $BACKEND_APP_HOME
+
+# install dependencies
+RUN apt-get update \
+    && apt-get -y install libpq-dev gcc \
+    && pip install psycopg
+
+COPY --from=builder /app/wheels /wheels
+COPY --from=builder /app/requirements.txt .
+RUN pip install --upgrade pip
+RUN pip install --no-cache /wheels/*
+
+# copy project
+COPY . $BACKEND_APP_HOME
+
+# chown all the files to the app user
+RUN chown -R app:app $BACKEND_APP_HOME
+
+# change to the app user
+USER app
+
+# Expose port
+EXPOSE 7860
+ENV GRADIO_SERVER_NAME="0.0.0.0"
+
+CMD ["gradio", "app.py"]

app.py

@@ -15,6 +15,7 @@ import gradio as gr
 import openai
 from dotenv import load_dotenv
 from slugify import slugify
+from cachetools import LRUCache
 
 from config import STUDY_FILES, OPENAI_API_KEY
 from rag.rag_pipeline import RAGPipeline
@@ -23,6 +24,7 @@ from utils.helpers import (
     add_study_files_to_chromadb,
     chromadb_client,
 )
+from utils.db import create_db_and_tables, add_study_files_to_db, get_study_file_by_name, get_study_files_by_library_id, get_all_study_files
 from utils.prompts import highlight_prompt, evidence_based_prompt
 from utils.zotero_manager import ZoteroManager
 
@@ -39,9 +41,25 @@ openai.api_key = OPENAI_API_KEY
 # Initialize ChromaDB with study files
 add_study_files_to_chromadb("study_files.json", "study_files_collection")
 
+# Create sqlite study file data table
+create_db_and_tables()
+
+
 # Cache for RAG pipelines
 rag_cache = {}
 
+cache = LRUCache(maxsize=100)
+
+# with open("study_files.json", "w") as file:
+#     data_ = {}
+#     json.dump(data_, file, indent=4)
+
+def get_cache_value(key):
+    return cache.get(key)
+
+zotero_library_id = get_cache_value("zotero_library_id")
+logger.info(f"zotero_library_id: ======> {zotero_library_id}")
+
 
 def get_rag_pipeline(study_name: str) -> RAGPipeline:
     """Get or create a RAGPipeline instance for the given study by querying ChromaDB."""
@@ -61,18 +79,26 @@ def get_rag_pipeline(study_name: str) -> RAGPipeline:
     return rag_cache[study_name]
 
 
-def get_study_info(study_name: str) -> str:
+def get_study_info(study_name: str | list) -> str:
     """Retrieve information about the specified study."""
+    if isinstance(study_name, list):
+        study_name = study_name[0] if study_name else None
+    
+    if not study_name:
+        return "No study selected"
+    
+    study = get_study_file_by_name(study_name)
+    logger.info(f"Study: ======> {study}")
 
     collection = chromadb_client.get_or_create_collection("study_files_collection")
     result = collection.get(ids=[study_name])  # Query by study name (as a list)
-    logging.info(f"Result: ======> {result}")
+    logger.info(f"Result: ======> {result}")
 
     if not result or len(result["metadatas"]) == 0:
         raise ValueError(f"Invalid study name: {study_name}")
 
     study_file = result["metadatas"][0].get("file_path")
-    logging.info(f"study_file: =======> {study_file}")
+    logger.info(f"study_file: =======> {study_file}")
     if not study_file:
         raise ValueError(f"File path not found for study name: {study_name}")
 
@@ -116,9 +142,9 @@ def cleanup_temp_files():
                     try:
                         os.remove(file)
                     except Exception as e:
-                        logging.warning(f"Failed to remove temp file {file}: {e}")
+                        logger.warning(f"Failed to remove temp file {file}: {e}")
     except Exception as e:
-        logging.warning(f"Error during cleanup: {e}")
+        logger.warning(f"Error during cleanup: {e}")
 
 
 def chat_function(message: str, study_name: str, prompt_type: str) -> str:
@@ -128,7 +154,7 @@ def chat_function(message: str, study_name: str, prompt_type: str) -> str:
         return "Please enter a valid query."
 
     rag = get_rag_pipeline(study_name)
-    logging.info(f"rag: ==> {rag}")
+    logger.info(f"rag: ==> {rag}")
     prompt = {
         "Highlight": highlight_prompt,
         "Evidence-based": evidence_based_prompt,
@@ -139,12 +165,14 @@ def chat_function(message: str, study_name: str, prompt_type: str) -> str:
 
 
 def process_zotero_library_items(
-    zotero_library_id: str, zotero_api_access_key: str
+    zotero_library_id_param: str, zotero_api_access_key: str
 ) -> str:
-    if not zotero_library_id or not zotero_api_access_key:
+    global zotero_library_id
+    if not zotero_library_id_param or not zotero_api_access_key:
         return "Please enter your zotero library Id and API Access Key"
 
-    zotero_library_id = zotero_library_id
+    zotero_library_id = zotero_library_id_param
+    cache["zotero_library_id"] = zotero_library_id
     zotero_library_type = "user"  # or "group"
     zotero_api_access_key = zotero_api_access_key
 
@@ -192,10 +220,16 @@ def process_zotero_library_items(
 
                 # Update in-memory STUDY_FILES for reference in current session
                 STUDY_FILES.update({collection_name: f"data/{export_file}"})
-                logging.info(f"STUDY_FILES: {STUDY_FILES}")
+                logger.info(f"STUDY_FILES: {STUDY_FILES}")
 
         # After loop, add all collected data to ChromaDB
         add_study_files_to_chromadb("study_files.json", "study_files_collection")
+        # Add collected data to sqlite
+        add_study_files_to_db("study_files.json", zotero_library_id)
+
+        # Dynamically update study choices
+        global study_choices
+        study_choices = [file.name for file in get_study_files_by_library_id([zotero_library_id])]
         message = "Successfully processed items in your zotero library"
     except Exception as e:
         message = f"Error process your zotero library: {str(e)}"
@@ -203,11 +237,25 @@ def process_zotero_library_items(
     return message
 
 
+def refresh_study_choices():
+    """
+    Refresh study choices for a specific dropdown instance.
+    
+    :return: Updated Dropdown with current study choices
+    """
+    global study_choices
+    zotero_library_id = get_cache_value("zotero_library_id")
+    logger.info(f"zotero_library_id: ====> {zotero_library_id}")
+    study_choices = [file.name for file in get_study_files_by_library_id([zotero_library_id])]
+    logger.info(f"Study choices: ====> {study_choices}")
+    return study_choices
+
+
 def process_multi_input(text, study_name, prompt_type):
     # Split input based on commas and strip any extra spaces
     variable_list = [word.strip().upper() for word in text.split(",")]
     user_message = f"Extract and present in a tabular format the following variables for each {study_name} study: {', '.join(variable_list)}"
-    logging.info(f"User message: ==> {user_message}")
+    logger.info(f"User message: ==> {user_message}")
     response = chat_function(user_message, study_name, prompt_type)
     return [response, gr.update(visible=True)]
 
@@ -311,7 +359,8 @@ def chat_response(
 
 def create_gr_interface() -> gr.Blocks:
     """Create and configure the Gradio interface for the RAG platform."""
-    with gr.Blocks() as demo:
+    global zotero_library_id
+    with gr.Blocks(theme=gr.themes.Base()) as demo:
         gr.Markdown("# ACRES RAG Platform")
 
         with gr.Tabs() as tabs:
@@ -320,7 +369,7 @@ def create_gr_interface() -> gr.Blocks:
                 with gr.Row():
                     with gr.Column(scale=1):
                         gr.Markdown("### Zotero Credentials")
-                        zotero_library_id = gr.Textbox(
+                        zotero_library_id_param = gr.Textbox(
                             label="Zotero Library ID",
                             type="password",
                             placeholder="Enter Your Zotero Library ID here...",
@@ -346,11 +395,24 @@ def create_gr_interface() -> gr.Blocks:
                             if all_documents
                         ]
 
+                        print(f"zotero_library_id: {zotero_library_id_param.value}")
+                        zotero_library_id = zotero_library_id_param.value
+                        if zotero_library_id is None:
+                            zotero_library_id = get_cache_value("zotero_library_id")
+                        logger.info(f"zotero_library_id: =====> {zotero_library_id}")
+                        study_choices_db = get_study_files_by_library_id([zotero_library_id])
+                        logger.info(f"study_choices_db: =====> {study_choices_db}")
+                        study_files = get_all_study_files()
+                        logger.info(f"study_files: =====> {study_files}")
+
                         study_dropdown = gr.Dropdown(
                             choices=study_choices,
                             label="Select Study",
                             value=(study_choices[0] if study_choices else None),
                         )
+                        # In Gradio interface setup
+                        refresh_button = gr.Button("Refresh Studies")
+
                         study_info = gr.Markdown(label="Study Details")
                         prompt_type = gr.Radio(
                             ["Default", "Highlight", "Evidence-based"],
@@ -420,7 +482,7 @@ def create_gr_interface() -> gr.Blocks:
         # Event handlers for Study Analysis tab
         process_zotero_btn.click(
             process_zotero_library_items,
-            inputs=[zotero_library_id, zotero_api_access_key],
+            inputs=[zotero_library_id_param, zotero_api_access_key],
             outputs=[zotero_output],
         )
 
@@ -438,6 +500,11 @@ def create_gr_interface() -> gr.Blocks:
             fn=download_as_csv, inputs=[answer_output], outputs=[download_btn]
         ).then(fn=cleanup_temp_files, inputs=None, outputs=None)
 
+        refresh_button.click(
+            fn=refresh_study_choices, 
+            outputs=[study_dropdown]  # Update the same dropdown
+        )
+
         # Event handlers for PDF Chat tab
 
         def handle_pdf_upload(files, name):

bin/cfn/ecs-delete

@@ -0,0 +1,14 @@
+#! /usr/bin/env bash
+set -e # stop the execution of the script if it fails
+
+CONFIG_PATH="/Users/patrickcmd/Projects/sunbirdai/Acres/infra/ecs_config.toml"
+
+
+REGION=$(cfn-toml key deploy.region -t $CONFIG_PATH)
+STACK_NAME=$(cfn-toml key deploy.stack_name -t $CONFIG_PATH)
+
+
+aws cloudformation delete-stack \
+    --stack-name $STACK_NAME \
+    --region $REGION \
+    --profile sunbirdai

bin/cfn/ecs-deploy

@@ -0,0 +1,25 @@
+#! /usr/bin/env bash
+set -e # stop the execution of the script if it fails
+
+CFN_PATH="/Users/patrickcmd/Projects/sunbirdai/Acres/infra/ecs_fargate.yml"
+CONFIG_PATH="/Users/patrickcmd/Projects/sunbirdai/Acres/infra/ecs_config.toml"
+echo $CFN_PATH
+
+cfn-lint $CFN_PATH
+
+BUCKET=$(cfn-toml key deploy.bucket -t $CONFIG_PATH)
+REGION=$(cfn-toml key deploy.region -t $CONFIG_PATH)
+STACK_NAME=$(cfn-toml key deploy.stack_name -t $CONFIG_PATH)
+PARAMETERS=$(cfn-toml params v2 -t $CONFIG_PATH)
+
+aws cloudformation deploy \
+  --stack-name $STACK_NAME \
+  --s3-bucket $BUCKET \
+  --s3-prefix acres-rag \
+  --region $REGION \
+  --template-file "$CFN_PATH" \
+  --no-execute-changeset \
+  --tags group=acres-rag \
+  --parameter-overrides $PARAMETERS \
+  --capabilities CAPABILITY_NAMED_IAM \
+  --profile sunbirdai

commands.md

@@ -0,0 +1,69 @@
+docker network create gradio-fastapi-network
+
+docker run -it -p 7860:7860 --rm --name gradio --network=gradio-fastapi-network gradio-app
+
+docker run -it -p 7860:7860 --rm --name gradio --network=gradio-fastapi-network gradio-app-prod
+
+
+export AWS_DEFAULT_REGION=us-east-1
+export AWS_ACCOUNT_ID=224427659724
+aws ecr get-login-password --region $AWS_DEFAULT_REGION | docker login --username AWS --password-stdin "$AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com"
+
+aws ecr create-repository \
+  --repository-name gradio-python \
+  --image-tag-mutability MUTABLE
+
+export ECR_PYTHON_URL="$AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/gradio-python"
+echo $ECR_PYTHON_URL
+
+docker pull python:3.11.10-slim
+docker tag python:3.11.10-slim $ECR_PYTHON_URL:3.11.10-slim
+
+docker push $ECR_PYTHON_URL:3.11.10-slim
+
+
+aws ecr create-repository \
+  --repository-name gradio-app-prod \
+  --image-tag-mutability MUTABLE
+
+export ECR_BACKEND_GRADIO_URL="$AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/gradio-app-prod"
+echo $ECR_BACKEND_GRADIO_URL
+
+
+docker build -f Dockerfile.gradio.prod -t gradio-app-prod .
+docker tag gradio-app-prod:latest "${ECR_BACKEND_GRADIO_URL}:latest"
+docker push "${ECR_BACKEND_GRADIO_URL}:latest"
+
+
+docker build -f Dockerfile.api -t fastapi-app .
+docker run -it -p 8000:8000 --rm --name fastapi --network=gradio-fastapi-network fastapi-app
+
+aws ecr create-repository \
+  --repository-name fastapi-api-prod \
+  --image-tag-mutability MUTABLE
+
+export ECR_BACKEND_FASTAPI_URL="$AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/fastapi-api-prod"
+echo $ECR_BACKEND_FASTAPI_URL
+
+docker build -f Dockerfile.api.prod -t fastapi-api-prod .
+docker tag fastapi-api-prod:latest "${ECR_BACKEND_FASTAPI_URL}:latest"
+docker push "${ECR_BACKEND_FASTAPI_URL}:latest"
+
+
+Now how can I configure the two load balancers such that I can just access them without providing the ports
+
+fastapi
+
+
+```
+http://dev-acres-fastapi-alb-1793670355.us-east-1.elb.amazonaws.com:8000/
+```
+
+http://dev-acres-gradio-alb-1860302806.us-east-1.elb.amazonaws.com/
+
+gradio
+
+
+```
+http://dev-acres-gradio-alb-1860302806.us-east-1.elb.amazonaws.com:7860/
+```

infra/ecs_config.toml

@@ -0,0 +1,9 @@
+[deploy]
+bucket = 'dev-acres-gradio-bucket'
+region = 'us-east-1'
+stack_name = 'AcresRag'
+
+[parameters]
+ContainerImageGradio = '224427659724.dkr.ecr.us-east-1.amazonaws.com/gradio-app-prod:latest'
+ContainerImageFastAPI = '224427659724.dkr.ecr.us-east-1.amazonaws.com/fastapi-api-prod:latest'
+CertificateArn = 'arn:aws:acm:us-east-1:224427659724:certificate/37ae35a9-60d1-4ff2-8afc-07f0d6000e75'

infra/ecs_fargate.yml

@@ -0,0 +1,581 @@
+AWSTemplateFormatVersion: '2010-09-09'
+Description: Deploy Gradio and FastAPI services on AWS ECS Fargate
+
+Parameters:
+  Environment:
+    Type: String
+    Default: dev
+    AllowedValues: [dev, prod]
+  
+  # VPC Configuration
+  VpcCIDR:
+    Type: String
+    Default: 10.0.0.0/16
+  PublicSubnet1CIDR:
+    Type: String
+    Default: 10.0.1.0/24
+  PublicSubnet2CIDR:
+    Type: String
+    Default: 10.0.2.0/24
+  
+  # ECS Configuration
+  ECSClusterName:
+    Type: String
+    Default: rag-ecs-cluster
+  GradioTaskDefinitionCPU:
+    Type: Number
+    Default: 512
+  GradioTaskDefinitionMemory:
+    Type: Number 
+    Default: 1024
+  FastAPITaskDefinitionCPU:
+    Type: Number
+    Default: 256
+  FastAPITaskDefinitionMemory: 
+    Type: Number
+    Default: 512
+  
+  # Container Images
+  ContainerImageGradio:
+    Type: String
+    Description: URI of the Gradio container image in ECR
+  ContainerImageFastAPI:
+    Type: String
+    Description: URI of the FastAPI container image in ECR
+  # CertificateArn:
+  #   Type: String
+
+Resources:
+  # VPC and Networking
+  VPC:
+    Type: AWS::EC2::VPC
+    Properties:
+      CidrBlock: !Ref VpcCIDR
+      EnableDnsHostnames: true
+      EnableDnsSupport: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${Environment}-acres-vpc
+
+  InternetGateway:
+    Type: AWS::EC2::InternetGateway
+    Properties:
+      Tags:
+        - Key: Name
+          Value: !Sub ${Environment}-acres-igw
+
+  AttachGateway:
+    Type: AWS::EC2::VPCGatewayAttachment
+    Properties:
+      VpcId: !Ref VPC
+      InternetGatewayId: !Ref InternetGateway
+
+  PublicSubnet1:
+    Type: AWS::EC2::Subnet
+    Properties:
+      VpcId: !Ref VPC
+      AvailabilityZone: !Select [0, !GetAZs '']
+      CidrBlock: !Ref PublicSubnet1CIDR
+      MapPublicIpOnLaunch: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${Environment}-acres-public-subnet-1
+
+  PublicSubnet2:
+    Type: AWS::EC2::Subnet
+    Properties:
+      VpcId: !Ref VPC
+      AvailabilityZone: !Select [1, !GetAZs '']
+      CidrBlock: !Ref PublicSubnet2CIDR
+      MapPublicIpOnLaunch: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${Environment}-acres-public-subnet-2
+
+  PublicRouteTable:
+    Type: AWS::EC2::RouteTable
+    Properties:
+      VpcId: !Ref VPC
+      Tags:
+        - Key: Name
+          Value: !Sub ${Environment}-acres-public-rt
+
+  PublicRoute:
+    Type: AWS::EC2::Route
+    DependsOn: AttachGateway
+    Properties:
+      RouteTableId: !Ref PublicRouteTable
+      DestinationCidrBlock: 0.0.0.0/0
+      GatewayId: !Ref InternetGateway
+
+  PublicSubnet1RouteTableAssociation:
+    Type: AWS::EC2::SubnetRouteTableAssociation
+    Properties:
+      SubnetId: !Ref PublicSubnet1
+      RouteTableId: !Ref PublicRouteTable
+
+  PublicSubnet2RouteTableAssociation:
+    Type: AWS::EC2::SubnetRouteTableAssociation
+    Properties:
+      SubnetId: !Ref PublicSubnet2
+      RouteTableId: !Ref PublicRouteTable
+
+  # Security Groups
+  GradioSecurityGroup:
+    Type: AWS::EC2::SecurityGroup
+    Properties:
+      GroupDescription: Security group for Gradio service
+      VpcId: !Ref VPC
+      SecurityGroupIngress:
+        - IpProtocol: tcp
+          FromPort: 7860
+          ToPort: 7860
+          CidrIp: 0.0.0.0/0
+          Description: INTERNET HTTPS
+        - IpProtocol: tcp
+          FromPort: 80
+          ToPort: 80
+          CidrIp: 0.0.0.0/0
+          Description: INTERNET HTTP
+      SecurityGroupEgress:
+        - IpProtocol: -1
+          CidrIp: 0.0.0.0/0
+  
+  FastAPISecurityGroup:
+    Type: AWS::EC2::SecurityGroup
+    Properties:
+      GroupDescription: Security group for FastAPI service
+      VpcId: !Ref VPC
+      SecurityGroupIngress:
+        - IpProtocol: tcp
+          FromPort: 8000
+          ToPort: 8000
+          CidrIp: 0.0.0.0/0
+          Description: INTERNET HTTPS
+        - IpProtocol: tcp
+          FromPort: 80
+          ToPort: 80
+          CidrIp: 0.0.0.0/0
+          Description: INTERNET HTTP
+      SecurityGroupEgress:
+        - IpProtocol: -1
+          CidrIp: 0.0.0.0/0
+
+
+  # IAM Roles and Policies
+  # Gradio Execution Role - for pulling images and logging
+  GradioTaskExecutionRole:
+    Type: AWS::IAM::Role
+    Properties:
+      AssumeRolePolicyDocument:
+        Version: '2012-10-17'
+        Statement:
+          - Effect: Allow
+            Principal:
+              Service: ecs-tasks.amazonaws.com
+            Action: sts:AssumeRole
+      ManagedPolicyArns:
+        - arn:aws:iam::aws:policy/service-role/AmazonECSTaskExecutionRolePolicy
+      Policies:
+        - PolicyName: GradioExecutionPolicy
+          PolicyDocument:
+            Version: '2012-10-17'
+            Statement:
+              - Effect: Allow
+                Action:
+                  - ecr:GetAuthorizationToken
+                  - ecr:BatchCheckLayerAvailability
+                  - ecr:GetDownloadUrlForLayer
+                  - ecr:BatchGetImage
+                Resource: '*'
+              - Effect: Allow
+                Action:
+                  - logs:CreateLogStream
+                  - logs:PutLogEvents
+                Resource: 
+                  - !Sub arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/ecs/${Environment}-acres-gradio:*
+                  - !Sub arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/ecs/${Environment}-acres-gradio:log-stream:*
+
+  # Gradio Task Role - for runtime permissions
+  GradioTaskRole:
+    Type: AWS::IAM::Role
+    Properties:
+      AssumeRolePolicyDocument:
+        Version: '2012-10-17'
+        Statement:
+          - Effect: Allow
+            Principal:
+              Service: ecs-tasks.amazonaws.com
+            Action: sts:AssumeRole
+      Policies:
+        - PolicyName: GradioTaskPolicy
+          PolicyDocument:
+            Version: '2012-10-17'
+            Statement:
+              # Add specific permissions needed by your Gradio application at runtime
+              - Effect: Allow
+                Action:
+                  - s3:GetObject
+                  - s3:PutObject
+                Resource: !Sub arn:aws:s3:::${Environment}-acres-gradio-bucket/*
+  
+  # FastAPI Execution Role - for pulling images and logging
+  FastAPITaskExecutionRole:
+    Type: AWS::IAM::Role
+    Properties:
+      AssumeRolePolicyDocument:
+        Version: '2012-10-17'
+        Statement:
+          - Effect: Allow
+            Principal:
+              Service: ecs-tasks.amazonaws.com
+            Action: sts:AssumeRole
+      ManagedPolicyArns:
+        - arn:aws:iam::aws:policy/service-role/AmazonECSTaskExecutionRolePolicy
+      Policies:
+        - PolicyName: FastAPIExecutionPolicy
+          PolicyDocument:
+            Version: '2012-10-17'
+            Statement:
+              - Effect: Allow
+                Action:
+                  - ecr:GetAuthorizationToken
+                  - ecr:BatchCheckLayerAvailability
+                  - ecr:GetDownloadUrlForLayer
+                  - ecr:BatchGetImage
+                Resource: '*'
+              - Effect: Allow
+                Action:
+                  - logs:CreateLogStream
+                  - logs:PutLogEvents
+                Resource: 
+                  - !Sub arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/ecs/${Environment}-acres-fastapi:*
+                  - !Sub arn:aws:logs:${AWS::Region}:${AWS::AccountId}:log-group:/ecs/${Environment}-acres-fastapi:log-stream:*
+  
+  # FastAPI Task Role - for runtime permissions
+  FastAPITaskRole:
+    Type: AWS::IAM::Role
+    Properties:
+      AssumeRolePolicyDocument:
+        Version: '2012-10-17'
+        Statement:
+          - Effect: Allow
+            Principal:
+              Service: ecs-tasks.amazonaws.com
+            Action: sts:AssumeRole
+      Policies:
+        - PolicyName: FastAPITaskPolicy
+          PolicyDocument:
+            Version: '2012-10-17'
+            Statement:
+              # Add specific permissions needed by your FastAPI application at runtime
+              - Effect: Allow
+                Action:
+                  - dynamodb:GetItem
+                  - dynamodb:PutItem
+                  - dynamodb:Query
+                Resource: !Sub arn:aws:dynamodb:${AWS::Region}:${AWS::AccountId}:table/${Environment}-acres-fastapi-table
+              # Allow FastAPI to make HTTP calls to Gradio service
+              - Effect: Allow
+                Action:
+                  - execute-api:Invoke
+                Resource: !Sub arn:aws:execute-api:${AWS::Region}:${AWS::AccountId}:*
+
+  # ECS Cluster
+  ECSCluster:
+    Type: AWS::ECS::Cluster
+    Properties:
+      ClusterName: !Ref ECSClusterName
+      Tags:
+        - Key: Environment
+          Value: !Ref Environment
+
+  # Load Balancer for Gradio
+  GradioALB:
+    Type: AWS::ElasticLoadBalancingV2::LoadBalancer
+    Properties:
+      Name: !Sub ${Environment}-acres-gradio-alb
+      Scheme: internet-facing
+      LoadBalancerAttributes:
+        - Key: idle_timeout.timeout_seconds
+          Value: '60'
+      Subnets:
+        - !Ref PublicSubnet1
+        - !Ref PublicSubnet2
+      SecurityGroups:
+        - !Ref GradioSecurityGroup
+
+  GradioTargetGroup:
+    Type: AWS::ElasticLoadBalancingV2::TargetGroup
+    Properties:
+      HealthCheckEnabled: true
+      HealthCheckIntervalSeconds: 30
+      HealthCheckPath: /
+      HealthCheckPort: 7860
+      HealthCheckTimeoutSeconds: 20
+      HealthyThresholdCount: 2
+      Name: !Sub ${Environment}-acres-gradio-tg
+      Port: 7860
+      Protocol: HTTP
+      TargetType: ip
+      UnhealthyThresholdCount: 5
+      VpcId: !Ref VPC
+      TargetGroupAttributes:
+        - Key: deregistration_delay.timeout_seconds
+          Value: '30'
+
+  GradioHTTPSListener:
+    # https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-elasticloadbalancingv2-listener.html
+    Type: AWS::ElasticLoadBalancingV2::Listener
+    Properties:
+      DefaultActions:
+        - Type: forward
+          TargetGroupArn: !Ref GradioTargetGroup
+      LoadBalancerArn: !Ref GradioALB
+      # Certificates:
+      #   - CertificateArn: !Ref CertificateArn
+      Port: 7860
+      Protocol: HTTP
+  # GradioHTTPListener:
+  #   # https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-elasticloadbalancingv2-listener.html
+  #   Type: AWS::ElasticLoadBalancingV2::Listener
+  #   Properties:
+  #     Protocol: HTTP
+  #     Port: 80
+  #     LoadBalancerArn: !Ref GradioALB
+  #     DefaultActions:
+  #       - Type: redirect
+  #         RedirectConfig:
+  #           Protocol: "HTTPS"
+  #           Port: 7860
+  #           Host: "#{host}"
+  #           Path: "/#{path}"
+  #           Query: "#{query}"
+  #           StatusCode: "HTTP_301"
+  
+  # Load Balancer for FastAPI
+  FastAPIALB:
+    Type: AWS::ElasticLoadBalancingV2::LoadBalancer
+    Properties:
+      Name: !Sub ${Environment}-acres-fastapi-alb
+      Scheme: internet-facing
+      LoadBalancerAttributes:
+        - Key: idle_timeout.timeout_seconds
+          Value: '60'
+      Subnets:
+        - !Ref PublicSubnet1
+        - !Ref PublicSubnet2
+      SecurityGroups:
+        - !Ref FastAPISecurityGroup
+
+  FastAPITargetGroup:
+    Type: AWS::ElasticLoadBalancingV2::TargetGroup
+    Properties:
+      HealthCheckEnabled: true
+      HealthCheckIntervalSeconds: 30
+      HealthCheckPath: /docs  # FastAPI's Swagger UI path
+      HealthCheckPort: 8000
+      HealthCheckTimeoutSeconds: 20
+      HealthyThresholdCount: 2
+      Name: !Sub ${Environment}-acres-fastapi-tg
+      Port: 8000
+      Protocol: HTTP
+      TargetType: ip
+      UnhealthyThresholdCount: 5
+      VpcId: !Ref VPC
+      TargetGroupAttributes:
+        - Key: deregistration_delay.timeout_seconds
+          Value: '30'
+
+  FastAPIHTTPSListener:
+    # https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-elasticloadbalancingv2-listener.html
+    Type: AWS::ElasticLoadBalancingV2::Listener
+    Properties:
+      DefaultActions:
+        - Type: forward
+          TargetGroupArn: !Ref FastAPITargetGroup
+      LoadBalancerArn: !Ref FastAPIALB
+      # Certificates:
+      #   - CertificateArn: !Ref CertificateArn
+      Port: 8000
+      Protocol: HTTP
+  # FastAPIHTTPListener:
+  #   # https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-elasticloadbalancingv2-listener.html
+  #   Type: AWS::ElasticLoadBalancingV2::Listener
+  #   Properties:
+  #     Protocol: HTTP
+  #     Port: 80
+  #     LoadBalancerArn: !Ref FastAPIALB
+  #     DefaultActions:
+  #       - Type: redirect
+  #         RedirectConfig:
+  #           Protocol: "HTTPS"
+  #           Port: 8000
+  #           Host: "#{host}"
+  #           Path: "/#{path}"
+  #           Query: "#{query}"
+  #           StatusCode: "HTTP_301"
+
+  # ECS Task Definitions
+  GradioTaskDefinition:
+    Type: AWS::ECS::TaskDefinition
+    Properties:
+      Family: !Sub ${Environment}-acres-gradio
+      RequiresCompatibilities:
+        - FARGATE
+      Cpu: !Ref GradioTaskDefinitionCPU
+      Memory: !Ref GradioTaskDefinitionMemory
+      NetworkMode: awsvpc
+      ExecutionRoleArn: !GetAtt GradioTaskExecutionRole.Arn
+      TaskRoleArn: !GetAtt GradioTaskRole.Arn
+      ContainerDefinitions:
+        - Name: gradio
+          Image: !Ref ContainerImageGradio
+          PortMappings:
+            - ContainerPort: 7860
+          LogConfiguration:
+            LogDriver: awslogs
+            Options:
+              awslogs-group: !Ref GradioLogGroup
+              awslogs-region: !Ref AWS::Region
+              awslogs-stream-prefix: gradio
+  
+  FastAPITaskDefinition:
+    Type: AWS::ECS::TaskDefinition
+    Properties:
+      Family: !Sub ${Environment}-acres-fastapi
+      RequiresCompatibilities:
+        - FARGATE
+      Cpu: !Ref FastAPITaskDefinitionCPU
+      Memory: !Ref FastAPITaskDefinitionMemory
+      NetworkMode: awsvpc
+      ExecutionRoleArn: !GetAtt FastAPITaskExecutionRole.Arn
+      TaskRoleArn: !GetAtt FastAPITaskRole.Arn
+      ContainerDefinitions:
+        - Name: fastapi
+          Image: !Ref ContainerImageFastAPI
+          PortMappings:
+            - ContainerPort: 8000
+          Environment:
+            - Name: GRADIO_URL
+              Value: !Sub http://${GradioALB.DNSName}:7860/
+          LogConfiguration:
+            LogDriver: awslogs
+            Options:
+              awslogs-group: !Ref FastAPILogGroup
+              awslogs-region: !Ref AWS::Region
+              awslogs-stream-prefix: fastapi
+
+  # CloudWatch Log Groups
+  GradioLogGroup:
+    Type: AWS::Logs::LogGroup
+    Properties:
+      LogGroupName: !Sub /ecs/${Environment}-acres-gradio
+      RetentionInDays: 30
+  
+  FastAPILogGroup:
+    Type: AWS::Logs::LogGroup
+    Properties:
+      LogGroupName: !Sub /ecs/${Environment}-acres-fastapi
+      RetentionInDays: 30
+
+
+  # ECS Services
+  GradioService:
+    Type: AWS::ECS::Service
+    DependsOn: 
+      - GradioHTTPSListener
+      # - GradioHTTPListener
+    Properties:
+      ServiceName: !Sub ${Environment}-acres-gradio
+      Cluster: !Ref ECSCluster
+      TaskDefinition: !Ref GradioTaskDefinition
+      DesiredCount: 1
+      LaunchType: FARGATE
+      HealthCheckGracePeriodSeconds: 180
+      LoadBalancers:
+        - ContainerName: gradio
+          ContainerPort: 7860
+          TargetGroupArn: !Ref GradioTargetGroup
+      NetworkConfiguration:
+        AwsvpcConfiguration:
+          AssignPublicIp: ENABLED
+          SecurityGroups:
+            - !Ref GradioSecurityGroup
+          Subnets:
+            - !Ref PublicSubnet1
+            - !Ref PublicSubnet2
+      DeploymentConfiguration:
+        DeploymentCircuitBreaker:
+          Enable: true
+          Rollback: true
+        MaximumPercent: 200
+        MinimumHealthyPercent: 100
+  
+  FastAPIService:
+    Type: AWS::ECS::Service
+    DependsOn: 
+      - GradioService
+      - FastAPIHTTPSListener
+      # - FastAPIHTTPListener
+    Properties:
+      ServiceName: !Sub ${Environment}-acres-fastapi
+      Cluster: !Ref ECSCluster
+      TaskDefinition: !Ref FastAPITaskDefinition
+      DesiredCount: 1
+      LaunchType: FARGATE
+      HealthCheckGracePeriodSeconds: 180
+      LoadBalancers:
+        - ContainerName: fastapi
+          ContainerPort: 8000
+          TargetGroupArn: !Ref FastAPITargetGroup
+      NetworkConfiguration:
+        AwsvpcConfiguration:
+          AssignPublicIp: ENABLED
+          SecurityGroups:
+            - !Ref FastAPISecurityGroup
+          Subnets:
+            - !Ref PublicSubnet1
+            - !Ref PublicSubnet2
+      DeploymentConfiguration:
+        DeploymentCircuitBreaker:
+          Enable: true
+          Rollback: true
+        MaximumPercent: 200
+        MinimumHealthyPercent: 100
+      # Add deployment controller for better rollout control
+      DeploymentController:
+        Type: ECS
+
+Outputs:
+  VpcId:
+    Description: VPC ID
+    Value: !Ref VPC
+
+  PublicSubnet1:
+    Description: Public Subnet 1
+    Value: !Ref PublicSubnet1
+
+  PublicSubnet2:
+    Description: Public Subnet 2
+    Value: !Ref PublicSubnet2
+
+  GradioServiceUrl:
+    Description: URL for the Gradio service
+    Value: !Sub http://${GradioALB.DNSName}:7860/
+
+  ECSClusterName:
+    Description: Name of the ECS cluster
+    Value: !Ref ECSCluster
+
+  GradioServiceName:
+    Description: Name of the Gradio service
+    Value: !GetAtt GradioService.Name
+  
+  FastAPIServiceName:
+    Description: Name of the FastAPI service
+    Value: !GetAtt FastAPIService.Name
+  
+  FastAPIServiceUrl:
+    Description: URL for the FastAPI service
+    Value: !Sub http://${FastAPIALB.DNSName}:8000/

requirements.txt

@@ -1,5 +1,5 @@
-chromadb==0.5.5
-fastapi==0.112.2
+chromadb
+fastapi
 gradio
 gradio_client
 llama-index
@@ -12,4 +12,6 @@ python-dotenv
 pyzotero
 python-slugify
 PyMuPDF==1.23.8  
-Pillow==10.2.0 
+Pillow==10.2.0
+sqlmodel
+cachetools

study_files.json

@@ -1,10 +1,5 @@
 {
     "Vaccine coverage": "data/vaccine_coverage_zotero_items.json",
     "Ebola Virus": "data/ebola_virus_zotero_items.json",
-    "GeneXpert": "data/gene_xpert_zotero_items.json",
-    "Zotero Collection Pastan": "data/zotero-collection-pastan_zotero_items.json",
-    "EBSCOhost": "data/ebscohost_zotero_items.json",
-    "ExportedRis_file_1_of_1 (1)": "data/exportedris-file-1-of-1-1_zotero_items.json",
-    "wb_1813-9450-6689": "data/wb-1813-9450-6689_zotero_items.json",
-    "kayongo papers": "data/kayongo-papers_zotero_items.json"
+    "GeneXpert": "data/gene_xpert_zotero_items.json"
 }