Initial commit

omop/scripts/run_tests.sh

@@ -0,0 +1,73 @@
+#!/bin/bash
+# Test Execution Script for OMOP Data Pipeline
+# This script runs all tests with coverage reporting
+
+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
+
+echo -e "${GREEN}OMOP Pipeline Test Suite${NC}"
+echo "================================"
+echo ""
+
+# Check if pytest is installed
+if ! command -v pytest &> /dev/null; then
+    echo -e "${RED}Error: pytest not found${NC}"
+    echo "Please install test dependencies:"
+    echo "  pip install -e .[test]"
+    exit 1
+fi
+
+# Run tests with coverage
+echo -e "${YELLOW}Running tests with coverage...${NC}"
+echo ""
+
+pytest \
+    --verbose \
+    --cov=src \
+    --cov-report=html \
+    --cov-report=term \
+    --cov-report=xml \
+    tests/
+
+TEST_EXIT_CODE=$?
+
+echo ""
+if [ $TEST_EXIT_CODE -eq 0 ]; then
+    echo -e "${GREEN}================================${NC}"
+    echo -e "${GREEN}All tests passed!${NC}"
+    echo -e "${GREEN}================================${NC}"
+    echo ""
+    echo "Coverage report generated:"
+    echo "  HTML: htmlcov/index.html"
+    echo "  XML: coverage.xml"
+    echo ""
+else
+    echo -e "${RED}================================${NC}"
+    echo -e "${RED}Some tests failed${NC}"
+    echo -e "${RED}================================${NC}"
+    echo ""
+    exit $TEST_EXIT_CODE
+fi
+
+# Optional: Run linting
+if command -v flake8 &> /dev/null; then
+    echo -e "${YELLOW}Running code quality checks...${NC}"
+    flake8 src/ --max-line-length=100 --exclude=__pycache__,*.pyc
+    echo -e "${GREEN}✓ Code quality checks passed${NC}"
+    echo ""
+fi
+
+# Optional: Run type checking
+if command -v mypy &> /dev/null; then
+    echo -e "${YELLOW}Running type checks...${NC}"
+    mypy src/ --ignore-missing-imports
+    echo -e "${GREEN}✓ Type checks passed${NC}"
+    echo ""
+fi
+
+echo -e "${GREEN}Test suite completed successfully!${NC}"