74 lines
1.8 KiB
Bash
Executable File
74 lines
1.8 KiB
Bash
Executable File
#!/bin/bash
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# Test Execution Script for OMOP Data Pipeline
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# This script runs all tests with coverage reporting
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set -e # Exit on error
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# Colors for output
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RED='\033[0;31m'
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GREEN='\033[0;32m'
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YELLOW='\033[1;33m'
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NC='\033[0m' # No Color
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echo -e "${GREEN}OMOP Pipeline Test Suite${NC}"
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echo "================================"
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echo ""
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# Check if pytest is installed
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if ! command -v pytest &> /dev/null; then
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echo -e "${RED}Error: pytest not found${NC}"
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echo "Please install test dependencies:"
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echo " pip install -e .[test]"
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exit 1
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fi
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# Run tests with coverage
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echo -e "${YELLOW}Running tests with coverage...${NC}"
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echo ""
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pytest \
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--verbose \
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--cov=src \
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--cov-report=html \
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--cov-report=term \
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--cov-report=xml \
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tests/
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TEST_EXIT_CODE=$?
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echo ""
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if [ $TEST_EXIT_CODE -eq 0 ]; then
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echo -e "${GREEN}================================${NC}"
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echo -e "${GREEN}All tests passed!${NC}"
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echo -e "${GREEN}================================${NC}"
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echo ""
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echo "Coverage report generated:"
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echo " HTML: htmlcov/index.html"
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echo " XML: coverage.xml"
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echo ""
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else
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echo -e "${RED}================================${NC}"
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echo -e "${RED}Some tests failed${NC}"
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echo -e "${RED}================================${NC}"
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echo ""
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exit $TEST_EXIT_CODE
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fi
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# Optional: Run linting
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if command -v flake8 &> /dev/null; then
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echo -e "${YELLOW}Running code quality checks...${NC}"
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flake8 src/ --max-line-length=100 --exclude=__pycache__,*.pyc
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echo -e "${GREEN}✓ Code quality checks passed${NC}"
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echo ""
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fi
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# Optional: Run type checking
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if command -v mypy &> /dev/null; then
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echo -e "${YELLOW}Running type checks...${NC}"
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mypy src/ --ignore-missing-imports
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echo -e "${GREEN}✓ Type checks passed${NC}"
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echo ""
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fi
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echo -e "${GREEN}Test suite completed successfully!${NC}"
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