Add wait4x / logging

setup.sh

@@ -10,39 +10,44 @@ VOCAB_DATA_DIR="$VOCAB_DATA_DIR"
 SCHEMA_NAME="$SCHEMA_NAME"
 
 # SQL files
-sql_files=(pk.sql constraint.sql index.sql)
+sql_files=(primary-keys.sql constraints.sql indices.sql)
 vocab_tables=(DRUG_STRENGTH CONCEPT CONCEPT_RELATIONSHIP CONCEPT_ANCESTOR CONCEPT_SYNONYM VOCABULARY RELATIONSHIP CONCEPT_CLASS DOMAIN)
 
 # Directory paths
 script_dir="/scripts"
 temp_dir="/tmp"
 
+echo "Waiting for the Database.."
+wait4x tcp://${DB_HOST}:${DB_PORT} --timeout 60
+echo "Database is up - continuing.."
+
 # Check if the schema already exists
 schema_exists=$(PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$DB_USER" -d "$DB_NAME" -tAc "SELECT 1 FROM information_schema.schemata WHERE schema_name = '${SCHEMA_NAME}'")
 if [ "$schema_exists" ]; then
     echo "Schema '${SCHEMA_NAME}' already exists. Skipping CDM creation."
     exit 0  # Exit gracefully
 fi
 
-# Create schema
+echo "Creating schema.."
 PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$DB_USER" -d "$DB_NAME" -c "CREATE SCHEMA IF NOT EXISTS ${SCHEMA_NAME};"
 
-# Create tables 
+echo "Creating tables.."
 temp_ddl="${temp_dir}/temp_ddl.sql"
 sed "s/@cdmDatabaseSchema/${SCHEMA_NAME}/g" "${script_dir}/ddl.sql" > "$temp_ddl"
 PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$DB_USER" -d "$DB_NAME" -f "$temp_ddl"
 rm "$temp_ddl"
 
-# Load vocabs
+echo "Loading data.."
 for table in "${vocab_tables[@]}"; do
-    echo 'loading: ' $table
+    echo 'Loading: ' $table
     table_lower=$(echo "$table" | tr '[:upper:]' '[:lower:]')
     PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$DB_USER" -d "$DB_NAME" \
         -c "\COPY ${SCHEMA_NAME}.${table_lower} FROM '${VOCAB_DATA_DIR}/${table}.csv' WITH (FORMAT csv, DELIMITER E'\t', NULL '""', QUOTE E'\b', HEADER, ENCODING 'UTF8')"
 done
 
 # Create pk, constraints, indexes
 for sql_file in "${sql_files[@]}"; do
+    echo "Creating $sql_file.."
     input_file="${script_dir}/${sql_file}"
     temp_file="${temp_dir}/temp_${sql_file}"
 
@@ -51,3 +56,5 @@ for sql_file in "${sql_files[@]}"; do
     PGPASSWORD="$DB_PASSWORD" psql -h "$DB_HOST" -p "$DB_PORT" -U "$DB_USER" -d "$DB_NAME" -f "$temp_file"
     rm "$temp_file"
 done
+
+echo "OMOP CDM creation finished."