mCODE Translator

Running the Clinical Trial Data Fetcher

The clinical trial data fetcher can be run from the command line with various options:

Basic Usage

# Activate the conda environment first
conda activate mcode_translator

# Show help
python src/data_fetcher/fetcher.py --help

# Search for clinical trials
python src/data_fetcher/fetcher.py --condition "breast cancer" --limit 10

# Fetch a specific trial by NCT ID
python src/data_fetcher/fetcher.py --nct-id NCT00000000

# Export results to JSON file
python src/data_fetcher/fetcher.py --condition "lung cancer" --export results.json

# Process eligibility criteria with NLP engine
python src/data_fetcher/fetcher.py --nct-id NCT00000000 --process-criteria

# Search with pagination
python src/data_fetcher/fetcher.py --condition "breast cancer" --min-rank 50

# Calculate total number of studies
python src/data_fetcher/fetcher.py --condition "breast cancer" --count

Running Tests

Unit Tests

# Run unit tests for the fetcher
python -m pytest tests/unit/test_fetcher.py -v

# Run all unit tests
python -m pytest tests/unit/ -v

Integration Tests

# Run integration tests (including the new TestAPIIntegration class)
python -m pytest tests/integration/test_api_integration.py -v

# Run all integration tests
python -m pytest tests/integration/ -v

All Tests

# Run the complete test suite
python run_tests.py

Project Structure

• src/data_fetcher/fetcher.py - Main clinical trial data fetcher script
• tests/unit/test_fetcher.py - Unit tests for the fetcher
• tests/integration/test_api_integration.py - Integration tests including TestAPIIntegration class
• src/utils/config.py - Configuration management
• src/utils/cache.py - Caching mechanism
• src/nlp_engine/ - NLP processing components
• src/code_extraction/ - Code extraction components
• src/mcode_mapper/ - mCODE mapping components
• src/structured_data_generator/ - Structured data generation components

Dependencies

The project requires the following dependencies:

• requests>=2.25.1
• click>=7.1.2
• python-dotenv>=0.15.0
• spacy==3.7.5
• scispacy==0.5.4
• pytrials==0.3.0

Install with:

pip install -r requirements.txt

Testing Dependencies

• pytest>=6.0.0
• pytest-cov>=2.10.0
• pytest-html>=3.1.1
• coverage>=5.5

Install with:

pip install -r requirements-test.txt