feat: Update Dockerfile and scripts for Neo4j initialization and environment variable handling

Dockerfile

@@ -1,16 +1,29 @@
 # Hugging Face Space Dockerfile for MedGraphy
+# Runs Neo4j directly (no Docker-in-Docker)
 FROM python:3.10-slim
 
-# Install system dependencies
+# Install system dependencies including Java for Neo4j
 RUN apt-get update && apt-get install -y \
     wget \
     curl \
     git \
+    openjdk-17-jre-headless \
+    procps \
     && rm -rf /var/lib/apt/lists/*
 
-# Install Docker Compose (standalone binary for better compatibility with HF Spaces)
-RUN curl -L "https://github.com/docker/compose/releases/download/v2.23.0/docker-compose-linux-x86_64" -o /usr/local/bin/docker-compose && \
-    chmod +x /usr/local/bin/docker-compose
+# Download and install Neo4j
+RUN mkdir -p /neo4j && \
+    cd /neo4j && \
+    wget -q https://dist.neo4j.org/neo4j-community-5.15.0-unix.tar.gz && \
+    tar -xzf neo4j-community-5.15.0-unix.tar.gz && \
+    mv neo4j-community-5.15.0 neo4j-community && \
+    rm neo4j-community-5.15.0-unix.tar.gz
+
+# Configure Neo4j
+RUN cd /neo4j/neo4j-community && \
+    sed -i 's/#server.default_listen_address=0.0.0.0/server.default_listen_address=0.0.0.0/' conf/neo4j.conf && \
+    sed -i 's/#initial.dbms.default_database=neo4j/initial.dbms.default_database=neo4j/' conf/neo4j.conf && \
+    echo "dbms.security.auth_enabled=false" >> conf/neo4j.conf
 
 # Set working directory
 WORKDIR /app
@@ -21,22 +34,24 @@ RUN pip install --no-cache-dir -r requirements.txt
 
 COPY . .
 
-# Create data directory if it doesn't exist
-RUN mkdir -p data db
+# Create data directory
+RUN mkdir -p data db /tmp/medgraph
 
 # Make startup script executable
 RUN chmod +x startup.sh
 
-# Expose Gradio port
-EXPOSE 7860
+# Expose ports
+EXPOSE 7860 7474 7687
 
-# Set environment variables for local Neo4j
+# Set environment variables
 ENV NEO4J_URI=bolt://localhost:7687
 ENV NEO4J_USERNAME=neo4j
-ENV NEO4J_PASSWORD=medgraph123
+ENV NEO4J_PASSWORD=neo4j
 ENV NEO4J_DATABASE=neo4j
 ENV GRADIO_SERVER_NAME=0.0.0.0
 ENV GRADIO_SERVER_PORT=7860
+ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64
+ENV NEO4J_HOME=/neo4j/neo4j-community
 
 # Run startup script
 CMD ["bash", "startup.sh"]

app.py

@@ -12,10 +12,10 @@ load_dotenv()
 
 # Load credentials from environment or Hugging Face Spaces secrets
 GROQ_API_KEY = os.getenv("GROQ_API_KEY")
-# Use local Neo4j instance running in Docker
+# Use local Neo4j instance running directly (not Docker)
 NEO4J_URI = os.getenv("NEO4J_URI", "bolt://localhost:7687")
 NEO4J_USER = os.getenv("NEO4J_USERNAME", "neo4j")
-NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD", "medgraph123")
+NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD", "neo4j")
 NEO4J_DATABASE = os.getenv("NEO4J_DATABASE", "neo4j")
 FAISS_INDEX_PATH = "db/medicine_embeddings.index"
 METADATA_PATH = "db/metadata.json"

init_neo4j.py

@@ -17,7 +17,7 @@ load_dotenv()
 # Configuration
 NEO4J_URI = os.getenv("NEO4J_URI", "bolt://localhost:7687")
 NEO4J_USER = os.getenv("NEO4J_USERNAME", "neo4j")
-NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD", "medgraph123")
+NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD", "neo4j")
 EMBEDDING_MODEL = "all-MiniLM-L6-v2"
 VECTOR_INDEX_NAME = "medicine_embeddings"
 CSV_PATH = "data/Medicine_Details.csv"

startup.sh

@@ -3,21 +3,22 @@ set -e
 
 echo "🚀 Starting MedGraphy application..."
 
-# Create data marker directory if it doesn't exist
+# Create necessary directories
 mkdir -p /tmp/medgraph
 
-# Check if Neo4j data has been initialized before
+# Check if already initialized
 if [ -f "/tmp/medgraph/neo4j_initialized.flag" ]; then
-    echo "✅ Found existing Neo4j initialization marker. Skipping data setup."
+    echo "✅ Found existing Neo4j data marker"
     SKIP_INIT=true
 else
-    echo "📊 First time setup detected - will initialize Neo4j with data..."
+    echo "📊 First time setup - will initialize Neo4j with data..."
     SKIP_INIT=false
 fi
 
-# Start Neo4j in the background using docker-compose
-echo "🐳 Starting Neo4j container..."
-docker-compose up -d neo4j
+# Start Neo4j directly (not via Docker)
+echo "🚀 Starting Neo4j..."
+export NEO4J_HOME=/neo4j/neo4j-community
+$NEO4J_HOME/bin/neo4j start
 
 # Wait for Neo4j to be ready
 echo "⏳ Waiting for Neo4j to be ready..."
@@ -36,8 +37,8 @@ done
 if [ $attempt -eq $max_attempts ]; then
     echo "❌ Neo4j failed to start within expected time"
     echo "📋 Neo4j logs:"
-    docker-compose logs neo4j
-    exit 1
+    cat $NEO4J_HOME/logs/neo4j.log 2>/dev/null || echo "No logs available"
+    # Continue anyway - app will work with FAISS only
 fi
 
 # Initialize data if needed
@@ -49,10 +50,7 @@ if [ "$SKIP_INIT" = false ]; then
         echo "✅ Neo4j initialization complete!"
         touch /tmp/medgraph/neo4j_initialized.flag
     else
-        echo "❌ Neo4j initialization failed!"
-        echo "📋 Neo4j logs:"
-        docker-compose logs neo4j
-        exit 1
+        echo "⚠️ Neo4j initialization failed, continuing with FAISS only..."
     fi
 else
     echo "✅ Using existing Neo4j data"