Initial commit

omop/scripts/setup_database.sh

@@ -0,0 +1,91 @@
+#!/bin/bash
+# Database Setup Script for OMOP Data Pipeline
+# This script creates the database and schemas for the OMOP pipeline
+
+set -e  # Exit on error
+
+# Colors for output
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+NC='\033[0m' # No Color
+
+# Configuration (can be overridden by environment variables)
+DB_HOST="${DB_HOST:-localhost}"
+DB_PORT="${DB_PORT:-5432}"
+DB_NAME="${DB_NAME:-omop_db}"
+DB_USER="${DB_USER:-postgres}"
+DB_PASSWORD="${DB_PASSWORD:-}"
+ADMIN_USER="${ADMIN_USER:-postgres}"
+
+echo -e "${GREEN}OMOP Database Setup${NC}"
+echo "================================"
+echo "Host: $DB_HOST"
+echo "Port: $DB_PORT"
+echo "Database: $DB_NAME"
+echo "User: $DB_USER"
+echo "================================"
+echo ""
+
+# Check if PostgreSQL is running
+echo -e "${YELLOW}Checking PostgreSQL connection...${NC}"
+if ! pg_isready -h "$DB_HOST" -p "$DB_PORT" > /dev/null 2>&1; then
+    echo -e "${RED}Error: Cannot connect to PostgreSQL at $DB_HOST:$DB_PORT${NC}"
+    echo "Please ensure PostgreSQL is running and accessible."
+    exit 1
+fi
+echo -e "${GREEN}✓ PostgreSQL is running${NC}"
+echo ""
+
+# Create database if it doesn't exist
+echo -e "${YELLOW}Creating database...${NC}"
+if PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$ADMIN_USER" -lqt | cut -d \| -f 1 | grep -qw "$DB_NAME"; then
+    echo -e "${YELLOW}Database $DB_NAME already exists${NC}"
+else
+    PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$ADMIN_USER" -c "CREATE DATABASE $DB_NAME;"
+    echo -e "${GREEN}✓ Database $DB_NAME created${NC}"
+fi
+echo ""
+
+# Create user if it doesn't exist
+echo -e "${YELLOW}Creating database user...${NC}"
+if PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$ADMIN_USER" -d "$DB_NAME" -tAc "SELECT 1 FROM pg_roles WHERE rolname='$DB_USER'" | grep -q 1; then
+    echo -e "${YELLOW}User $DB_USER already exists${NC}"
+else
+    PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$ADMIN_USER" -d "$DB_NAME" -c "CREATE USER $DB_USER WITH PASSWORD '$DB_PASSWORD';"
+    echo -e "${GREEN}✓ User $DB_USER created${NC}"
+fi
+echo ""
+
+# Grant privileges
+echo -e "${YELLOW}Granting privileges...${NC}"
+PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$ADMIN_USER" -d "$DB_NAME" <<EOF
+GRANT ALL PRIVILEGES ON DATABASE $DB_NAME TO $DB_USER;
+GRANT ALL ON SCHEMA public TO $DB_USER;
+ALTER DEFAULT PRIVILEGES IN SCHEMA public GRANT ALL ON TABLES TO $DB_USER;
+ALTER DEFAULT PRIVILEGES IN SCHEMA public GRANT ALL ON SEQUENCES TO $DB_USER;
+EOF
+echo -e "${GREEN}✓ Privileges granted${NC}"
+echo ""
+
+# Create schemas using the Python CLI
+echo -e "${YELLOW}Creating OMOP schemas...${NC}"
+if command -v omop-pipeline &> /dev/null; then
+    omop-pipeline schema create --type all
+    echo -e "${GREEN}✓ OMOP schemas created${NC}"
+else
+    echo -e "${YELLOW}Warning: omop-pipeline command not found${NC}"
+    echo "Please install the package with: pip install -e ."
+    echo "Then run: omop-pipeline schema create --type all"
+fi
+echo ""
+
+echo -e "${GREEN}================================${NC}"
+echo -e "${GREEN}Database setup completed!${NC}"
+echo -e "${GREEN}================================${NC}"
+echo ""
+echo "Next steps:"
+echo "1. Load vocabularies: omop-pipeline vocab load --path /path/to/vocabularies"
+echo "2. Load staging data into staging tables"
+echo "3. Run ETL: omop-pipeline etl run --source staging.raw_patients --target person"
+echo ""