Trying to fix basic functionality again.

scripts/prepare_environment.sh

@@ -0,0 +1,127 @@
+#!/bin/bash
+# prepare_environment.sh
+#
+# This script prepares the environment for running the Synthea pipeline.
+# It rebuilds the Docker containers, ensures the directory structure is correct,
+# and starts the necessary services.
+
+set -e  # Exit on error
+
+# Display a header
+echo "=================================================="
+echo "Synthea All Diseases Pipeline - Environment Setup"
+echo "=================================================="
+
+# Check for Docker
+if ! command -v docker &> /dev/null; then
+    echo "ERROR: Docker is not installed or not in the PATH."
+    echo "Please install Docker and try again."
+    exit 1
+fi
+
+# Check for docker-compose
+if ! command -v docker-compose &> /dev/null; then
+    echo "ERROR: docker-compose is not installed or not in the PATH."
+    echo "Please install docker-compose and try again."
+    exit 1
+fi
+
+# Create necessary directories if they don't exist
+echo "Creating required directories..."
+mkdir -p module_generator
+mkdir -p src/main/resources/modules
+mkdir -p src/main/resources/disease
+mkdir -p modules
+mkdir -p output
+
+# Check if the module_generator directory has the required scripts
+if [ ! -f "module_generator/module_generator.py" ] || [ ! -f "module_generator/run_module_generator.py" ]; then
+    echo "ERROR: Required Python scripts not found in module_generator directory!"
+    # Check if they're in the python directory and we need to move them
+    if [ -d "python" ] && [ -f "python/module_generator.py" ] && [ -f "python/run_module_generator.py" ]; then
+        echo "Found scripts in python directory, moving them to module_generator directory..."
+        mkdir -p module_generator
+        mv python/module_generator.py module_generator/
+        mv python/run_module_generator.py module_generator/
+        # Copy README if exists
+        if [ -f "python/README_module_generator.md" ]; then
+            mv python/README_module_generator.md module_generator/
+        fi
+    else
+        echo "Scripts not found in python directory either. Please ensure the scripts are in the module_generator directory."
+        exit 1
+    fi
+fi
+
+# Make the Python scripts executable
+chmod +x module_generator/module_generator.py
+chmod +x module_generator/run_module_generator.py
+
+# Create symlinks for convenience
+ln -sf "$(pwd)/module_generator/run_module_generator.py" "$(pwd)/run_module_generator.py"
+ln -sf "$(pwd)/module_generator/module_generator.py" "$(pwd)/module_generator.py"
+
+# Create an empty disease_list.json if it doesn't exist
+if [ ! -f "src/main/resources/disease_list.json" ]; then
+    echo "Creating empty disease_list.json..."
+    echo "[]" > src/main/resources/disease_list.json
+fi
+
+# Check if .env file exists
+if [ ! -f ".env" ]; then
+    echo ".env file is missing. Creating from .env.example..."
+    if [ -f ".env.example" ]; then
+        cp .env.example .env
+        echo "   Created .env from .env.example. Please edit it with your API key."
+    else
+        echo "WARNING: .env.example not found. Creating minimal .env file..."
+        echo "ANTHROPIC_API_KEY=your_api_key_here" > .env
+    fi
+fi
+
+# Stop any running containers
+echo "Stopping any running containers..."
+docker-compose down || true
+
+# Rebuild the containers
+echo "Building Docker containers..."
+docker-compose build
+
+# Start the Synthea container
+echo "Starting Synthea container..."
+docker-compose up -d synthea
+
+# Give the container a moment to start
+echo "Waiting for Synthea container to be ready..."
+sleep 10
+
+# Check if the container is healthy
+CONTAINER_ID=$(docker-compose ps -q synthea)
+if [ -z "$CONTAINER_ID" ]; then
+    echo "ERROR: Failed to start Synthea container."
+    exit 1
+fi
+
+# Check if the container is using proper health checks
+HEALTH_STATUS=$(docker inspect --format='{{.State.Health.Status}}' $CONTAINER_ID 2>/dev/null || echo "unknown")
+if [ "$HEALTH_STATUS" != "healthy" ] && [ "$HEALTH_STATUS" != "unknown" ]; then
+    echo "WARNING: Synthea container is not reporting as healthy (status: $HEALTH_STATUS)."
+    echo "It may take some time for the container to become fully operational."
+    echo "You can proceed, but the pipeline may fail if the container is not ready."
+fi
+
+# Check if we should generate modules
+if [ "$1" == "--generate-modules" ]; then
+    echo "Starting module generator..."
+    docker-compose --profile generator up module-generator
+fi
+
+echo "=================================================="
+echo "Environment is ready!"
+echo ""
+echo "To generate patients for a disease module:"
+echo "nextflow run main.nf --disease_name \"Disease Name\" --generate_patients true"
+echo ""
+echo "To generate a new module and patients:"
+echo "nextflow run main.nf --disease_name \"Disease Name\" --force_generate true --generate_patients true"
+echo "=================================================="