gbanyan
4a80a0398e
- pyproject.toml: installable package with bioinformatics dependencies - Pydantic config schema with validation (ensembl_release >= 100, directory creation) - YAML config loader with override support - Default config with Ensembl 113, gnomAD v4.1 - 5 passing tests for config validation and hashing
136 lines
3.6 KiB
Python
136 lines
3.6 KiB
Python
"""Tests for configuration loading and validation."""
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from pathlib import Path
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import pytest
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from pydantic import ValidationError
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from usher_pipeline.config import load_config, load_config_with_overrides
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from usher_pipeline.config.schema import PipelineConfig
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def test_load_valid_config():
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"""Test loading valid default configuration."""
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config = load_config("config/default.yaml")
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assert isinstance(config, PipelineConfig)
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assert config.versions.ensembl_release == 113
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assert config.versions.gnomad_version == "v4.1"
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assert config.api.rate_limit_per_second == 5
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assert config.api.max_retries == 5
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assert config.scoring.gnomad == 0.20
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def test_invalid_config_missing_field(tmp_path):
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"""Test that missing required field raises ValidationError."""
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invalid_config = tmp_path / "invalid.yaml"
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invalid_config.write_text("""
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versions:
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ensembl_release: 113
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api:
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rate_limit_per_second: 5
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scoring:
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gnomad: 0.20
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""")
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with pytest.raises(ValidationError) as exc_info:
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load_config(invalid_config)
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# Check that error mentions missing field
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assert "data_dir" in str(exc_info.value)
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def test_invalid_ensembl_release(tmp_path):
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"""Test that ensembl_release < 100 raises ValidationError."""
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invalid_config = tmp_path / "invalid_ensembl.yaml"
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invalid_config.write_text("""
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data_dir: data
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cache_dir: data/cache
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duckdb_path: data/pipeline.duckdb
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versions:
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ensembl_release: 99
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gnomad_version: v4.1
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api:
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rate_limit_per_second: 5
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max_retries: 5
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cache_ttl_seconds: 86400
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timeout_seconds: 30
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scoring:
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gnomad: 0.20
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expression: 0.20
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annotation: 0.15
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localization: 0.15
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animal_model: 0.15
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literature: 0.15
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""")
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with pytest.raises(ValidationError) as exc_info:
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load_config(invalid_config)
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# Check that error mentions ensembl_release constraint
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error_str = str(exc_info.value)
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assert "ensembl_release" in error_str
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assert "greater than or equal to 100" in error_str.lower() or "100" in error_str
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def test_config_hash_deterministic():
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"""Test that config hash is deterministic and changes with config."""
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config1 = load_config("config/default.yaml")
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config2 = load_config("config/default.yaml")
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# Same config should produce same hash
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assert config1.config_hash() == config2.config_hash()
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# Hash should be SHA-256 (64 hex chars)
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assert len(config1.config_hash()) == 64
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# Different config should produce different hash
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config3 = load_config_with_overrides(
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"config/default.yaml",
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{"api.rate_limit_per_second": 10},
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)
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assert config3.config_hash() != config1.config_hash()
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def test_config_creates_directories(tmp_path):
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"""Test that loading config creates data and cache directories."""
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config_file = tmp_path / "test_config.yaml"
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# Use non-existent directories
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data_dir = tmp_path / "test_data"
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cache_dir = tmp_path / "test_cache"
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config_file.write_text(f"""
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data_dir: {data_dir}
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cache_dir: {cache_dir}
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duckdb_path: {tmp_path / "test.duckdb"}
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versions:
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ensembl_release: 113
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gnomad_version: v4.1
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api:
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rate_limit_per_second: 5
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max_retries: 5
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cache_ttl_seconds: 86400
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timeout_seconds: 30
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scoring:
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gnomad: 0.20
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expression: 0.20
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annotation: 0.15
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localization: 0.15
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animal_model: 0.15
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literature: 0.15
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""")
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# Directories should not exist before loading
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assert not data_dir.exists()
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assert not cache_dir.exists()
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# Load config
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config = load_config(config_file)
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# Directories should be created
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assert data_dir.exists()
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assert cache_dir.exists()
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assert data_dir.is_dir()
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assert cache_dir.is_dir()
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