glam/infrastructure/deploy-linkml.sh

#!/bin/bash
# Deploy LinkML Schema to PostgreSQL Database
# 
# This script:
# 1. Runs the SQL migration to create LinkML tables
# 2. Syncs the LinkML schema files to the server
# 3. Runs the Python loader to populate the database
# 4. Restarts the Postgres API service
#
# Usage: ./deploy-linkml.sh [--skip-migration] [--skip-sync] [--skip-load]

set -e

# Configuration
SERVER="91.98.224.44"
REMOTE_USER="root"
PROJECT_ROOT="$(cd "$(dirname "$0")/.." && pwd)"
LINKML_DIR="$PROJECT_ROOT/schemas/20251121/linkml"
SQL_DIR="$PROJECT_ROOT/infrastructure/sql"
SCRIPTS_DIR="$PROJECT_ROOT/scripts"

# Parse arguments
SKIP_MIGRATION=false
SKIP_SYNC=false
SKIP_LOAD=false

for arg in "$@"; do
    case $arg in
        --skip-migration)
            SKIP_MIGRATION=true
            ;;
        --skip-sync)
            SKIP_SYNC=true
            ;;
        --skip-load)
            SKIP_LOAD=true
            ;;
        --help|-h)
            echo "Usage: $0 [--skip-migration] [--skip-sync] [--skip-load]"
            echo ""
            echo "Options:"
            echo "  --skip-migration  Skip running SQL migration"
            echo "  --skip-sync       Skip syncing LinkML files to server"
            echo "  --skip-load       Skip running Python loader"
            exit 0
            ;;
    esac
done

echo "═══════════════════════════════════════════════════════════════"
echo "  LinkML Schema Deployment to PostgreSQL"
echo "═══════════════════════════════════════════════════════════════"
echo ""
echo "Server: $SERVER"
echo "LinkML Source: $LINKML_DIR"
echo ""

# Check SSH connectivity
echo "🔗 Testing SSH connection..."
if ! ssh -o ConnectTimeout=5 "$REMOTE_USER@$SERVER" "echo 'Connected'" 2>/dev/null; then
    echo "❌ Cannot connect to $SERVER"
    exit 1
fi
echo "   ✅ Connected"
echo ""

# Step 1: Run SQL migration
if [ "$SKIP_MIGRATION" = false ]; then
    echo "📦 Step 1: Running SQL migration..."
    
    if [ -f "$SQL_DIR/001_linkml_schema.sql" ]; then
        # Copy migration file to server
        scp "$SQL_DIR/001_linkml_schema.sql" "$REMOTE_USER@$SERVER:/tmp/"
        
        # Run migration
        ssh "$REMOTE_USER@$SERVER" "sudo -u postgres psql -d glam -f /tmp/001_linkml_schema.sql"
        
        echo "   ✅ Migration complete"
    else
        echo "   ⚠️ Migration file not found: $SQL_DIR/001_linkml_schema.sql"
    fi
    echo ""
else
    echo "⏭️  Skipping SQL migration"
    echo ""
fi

# Step 2: Sync LinkML files
if [ "$SKIP_SYNC" = false ]; then
    echo "📁 Step 2: Syncing LinkML schema files..."
    
    rsync -avz --progress --delete \
        --include="*.yaml" \
        --include="*/" \
        --exclude="__pycache__" \
        --exclude=".DS_Store" \
        "$LINKML_DIR/" \
        "$REMOTE_USER@$SERVER:/mnt/data/linkml/"
    
    echo "   ✅ Sync complete"
    echo ""
else
    echo "⏭️  Skipping LinkML file sync"
    echo ""
fi

# Step 3: Sync and run Python loader
if [ "$SKIP_LOAD" = false ]; then
    echo "🐍 Step 3: Running Python loader..."
    
    # Copy loader script to server
    scp "$SCRIPTS_DIR/load_linkml_to_postgres.py" "$REMOTE_USER@$SERVER:/tmp/"
    
    # Install dependencies if needed and run loader
    ssh "$REMOTE_USER@$SERVER" << 'EOF'
        cd /var/lib/glam/api
        
        # Activate virtual environment
        source venv/bin/activate
        
        # Install dependencies if needed
        pip install pyyaml asyncpg --quiet
        
        # Run loader
        export DATABASE_URL="postgresql://glam_api:glam_secret_2025@localhost:5432/glam"
        python /tmp/load_linkml_to_postgres.py \
            --version 20251121 \
            --schema-dir /mnt/data/linkml \
            --schema-name heritage_custodian
EOF
    
    echo "   ✅ Loader complete"
    echo ""
else
    echo "⏭️  Skipping Python loader"
    echo ""
fi

# Step 4: Sync updated API code and restart service
echo "🔄 Step 4: Updating Postgres API..."

# Copy updated main.py to the correct location
scp "$PROJECT_ROOT/backend/postgres/main.py" "$REMOTE_USER@$SERVER:/opt/glam-backend/postgres/main.py"

# Restart the service
ssh "$REMOTE_USER@$SERVER" "systemctl restart glam-postgres-api"

echo "   ✅ API updated"
echo ""

# Step 5: Verify deployment
echo "🔍 Step 5: Verifying deployment..."

# Check if tables exist
TABLES=$(ssh "$REMOTE_USER@$SERVER" "sudo -u postgres psql -d glam -t -c \"SELECT COUNT(*) FROM information_schema.tables WHERE table_name LIKE 'linkml_%'\"" | tr -d ' ')
echo "   LinkML tables: $TABLES"

# Check if data is loaded
CLASSES=$(ssh "$REMOTE_USER@$SERVER" "sudo -u postgres psql -d glam -t -c \"SELECT COUNT(*) FROM linkml_classes\" 2>/dev/null || echo '0'" | tr -d ' ')
SLOTS=$(ssh "$REMOTE_USER@$SERVER" "sudo -u postgres psql -d glam -t -c \"SELECT COUNT(*) FROM linkml_slots\" 2>/dev/null || echo '0'" | tr -d ' ')
ENUMS=$(ssh "$REMOTE_USER@$SERVER" "sudo -u postgres psql -d glam -t -c \"SELECT COUNT(*) FROM linkml_enums\" 2>/dev/null || echo '0'" | tr -d ' ')

echo "   Classes loaded: $CLASSES"
echo "   Slots loaded: $SLOTS"
echo "   Enums loaded: $ENUMS"
echo ""

echo "═══════════════════════════════════════════════════════════════"
echo "  Deployment Complete!"
echo "═══════════════════════════════════════════════════════════════"
echo ""
echo "API Endpoints:"
echo "  https://bronhouder.nl/api/postgres/linkml/versions"
echo "  https://bronhouder.nl/api/postgres/linkml/classes"
echo "  https://bronhouder.nl/api/postgres/linkml/slots"
echo "  https://bronhouder.nl/api/postgres/linkml/enums"
echo "  https://bronhouder.nl/api/postgres/linkml/search?q=Custodian"
echo "  https://bronhouder.nl/api/postgres/linkml/hierarchy"
echo ""
echo "Test with:"
echo "  curl https://bronhouder.nl/api/postgres/linkml/versions"
echo ""