"""Tests for NegBioDB Clinical Trial domain database layer.""" import sqlite3 import tempfile from pathlib import Path import pytest from negbiodb_ct.ct_db import ( create_ct_database, get_connection, refresh_all_ct_pairs, run_ct_migrations, ) MIGRATIONS_DIR = Path(__file__).resolve().parent.parent / "migrations_ct" @pytest.fixture def ct_db(tmp_path): """Create a temporary CT database with all migrations applied.""" db_path = tmp_path / "test_ct.db" run_ct_migrations(db_path, MIGRATIONS_DIR) return db_path class TestCTMigrations: """Test CT schema creation and migrations.""" def test_create_ct_database(self, tmp_path): db_path = tmp_path / "test.db" result = create_ct_database(db_path, MIGRATIONS_DIR) assert result == db_path assert db_path.exists() def test_migration_001_applied(self, ct_db): conn = get_connection(ct_db) try: versions = conn.execute( "SELECT version FROM schema_migrations" ).fetchall() assert ("001",) in versions finally: conn.close() def test_migration_002_applied(self, ct_db): conn = get_connection(ct_db) try: versions = conn.execute( "SELECT version FROM schema_migrations" ).fetchall() assert ("002",) in versions finally: conn.close() def test_idempotent_migrations(self, ct_db): """Running migrations twice should not fail.""" applied = run_ct_migrations(ct_db, MIGRATIONS_DIR) assert applied == [] # Nothing new to apply def test_all_tables_exist(self, ct_db): conn = get_connection(ct_db) try: tables = { row[0] for row in conn.execute( "SELECT name FROM sqlite_master WHERE type='table'" ).fetchall() } expected = { "schema_migrations", "dataset_versions", "interventions", "conditions", "intervention_targets", "clinical_trials", "trial_interventions", "trial_conditions", "trial_publications", "combination_components", "trial_failure_results", "intervention_condition_pairs", "trial_failure_context", } assert expected.issubset(tables), f"Missing: {expected - tables}" finally: conn.close() class TestCTSchema: """Test CT schema constraints and foreign keys.""" def test_interventions_type_check(self, ct_db): conn = get_connection(ct_db) try: conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'Imatinib')" ) conn.commit() with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('invalid_type', 'Bad')" ) finally: conn.close() def test_clinical_trial_unique_constraint(self, ct_db): conn = get_connection(ct_db) try: conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status) " "VALUES ('clinicaltrials_gov', 'NCT00000001', 'Terminated')" ) conn.commit() with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status) " "VALUES ('clinicaltrials_gov', 'NCT00000001', 'Completed')" ) finally: conn.close() def test_same_trial_id_different_source(self, ct_db): """Same trial ID from different registries should work.""" conn = get_connection(ct_db) try: conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status) " "VALUES ('clinicaltrials_gov', 'NCT00000001', 'Terminated')" ) conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status) " "VALUES ('eu_ctr', 'NCT00000001', 'Terminated')" ) conn.commit() count = conn.execute( "SELECT COUNT(*) FROM clinical_trials" ).fetchone()[0] assert count == 2 finally: conn.close() def test_failure_category_check(self, ct_db): conn = get_connection(ct_db) try: # Insert required FK rows conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'TestDrug')" ) conn.execute( "INSERT INTO conditions (condition_name) VALUES ('TestDisease')" ) conn.commit() # Valid category conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method) " "VALUES (1, 1, 'efficacy', 'gold', 'aact', 'NCT001', 'database_direct')" ) conn.commit() # Invalid category with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method) " "VALUES (1, 1, 'invalid', 'gold', 'aact', 'NCT002', 'database_direct')" ) finally: conn.close() def test_confidence_tier_check(self, ct_db): conn = get_connection(ct_db) try: conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'TestDrug')" ) conn.execute( "INSERT INTO conditions (condition_name) VALUES ('TestDisease')" ) conn.commit() with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method) " "VALUES (1, 1, 'efficacy', 'platinum', 'aact', 'NCT001', 'database_direct')" ) finally: conn.close() def test_foreign_key_enforcement(self, ct_db): """FK violations should raise errors.""" conn = get_connection(ct_db) try: with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method) " "VALUES (999, 999, 'efficacy', 'gold', 'aact', 'NCT001', 'database_direct')" ) finally: conn.close() class TestRefreshCTPairs: """Test intervention_condition_pairs aggregation.""" def _insert_test_data(self, conn): """Insert minimal test data for aggregation testing.""" conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'DrugA')" ) conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'DrugB')" ) conn.execute( "INSERT INTO conditions (condition_name) VALUES ('DiseaseX')" ) conn.execute( "INSERT INTO conditions (condition_name) VALUES ('DiseaseY')" ) conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status, trial_phase) " "VALUES ('clinicaltrials_gov', 'NCT001', 'Terminated', 'phase_3')" ) conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status, trial_phase) " "VALUES ('clinicaltrials_gov', 'NCT002', 'Completed', 'phase_2')" ) # DrugA + DiseaseX: 2 trials (gold + silver) conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, trial_id, failure_category, " " confidence_tier, source_db, source_record_id, extraction_method, " " publication_year, highest_phase_reached) " "VALUES (1, 1, 1, 'efficacy', 'gold', 'aact', 'R001', 'database_direct', 2020, 'phase_3')" ) conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, trial_id, failure_category, " " confidence_tier, source_db, source_record_id, extraction_method, " " publication_year, highest_phase_reached) " "VALUES (1, 1, 2, 'efficacy', 'silver', 'aact', 'R002', 'database_direct', 2022, 'phase_2')" ) # DrugA + DiseaseY: 1 trial (bronze) conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, " " confidence_tier, source_db, source_record_id, extraction_method, " " publication_year, highest_phase_reached) " "VALUES (1, 2, 'safety', 'bronze', 'aact', 'R003', 'nlp_classified', 2021, 'phase_2')" ) # DrugB + DiseaseX: 1 trial (copper) conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, " " confidence_tier, source_db, source_record_id, extraction_method, " " publication_year, highest_phase_reached) " "VALUES (2, 1, 'enrollment', 'copper', 'aact', 'R004', 'text_mining', 2023, 'phase_1')" ) conn.commit() def test_refresh_pair_count(self, ct_db): conn = get_connection(ct_db) try: self._insert_test_data(conn) count = refresh_all_ct_pairs(conn) conn.commit() assert count == 3 # 3 unique intervention-condition pairs finally: conn.close() def test_best_confidence_aggregation(self, ct_db): conn = get_connection(ct_db) try: self._insert_test_data(conn) refresh_all_ct_pairs(conn) conn.commit() row = conn.execute( "SELECT best_confidence, num_trials FROM intervention_condition_pairs " "WHERE intervention_id = 1 AND condition_id = 1" ).fetchone() assert row[0] == "gold" # best of gold + silver assert row[1] == 2 # 2 distinct trials finally: conn.close() def test_degree_computation(self, ct_db): conn = get_connection(ct_db) try: self._insert_test_data(conn) refresh_all_ct_pairs(conn) conn.commit() # DrugA tested on 2 conditions → intervention_degree = 2 row = conn.execute( "SELECT intervention_degree FROM intervention_condition_pairs " "WHERE intervention_id = 1 AND condition_id = 1" ).fetchone() assert row[0] == 2 # DiseaseX tested with 2 drugs → condition_degree = 2 row = conn.execute( "SELECT condition_degree FROM intervention_condition_pairs " "WHERE intervention_id = 1 AND condition_id = 1" ).fetchone() assert row[0] == 2 finally: conn.close() def test_refresh_is_idempotent(self, ct_db): conn = get_connection(ct_db) try: self._insert_test_data(conn) count1 = refresh_all_ct_pairs(conn) conn.commit() count2 = refresh_all_ct_pairs(conn) conn.commit() assert count1 == count2 finally: conn.close() def test_highest_phase_ordering(self, ct_db): """CASE-based phase ordering should pick phase_3 over not_applicable.""" conn = get_connection(ct_db) try: conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'DrugX')" ) conn.execute( "INSERT INTO conditions (condition_name) VALUES ('DiseaseZ')" ) conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status) " "VALUES ('clinicaltrials_gov', 'NCT100', 'Terminated')" ) conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status) " "VALUES ('clinicaltrials_gov', 'NCT101', 'Terminated')" ) # Result 1: not_applicable phase conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, trial_id, failure_category, " " confidence_tier, source_db, source_record_id, extraction_method, " " highest_phase_reached) " "VALUES (1, 1, 1, 'efficacy', 'bronze', 'aact', 'P001', " "'nlp_classified', 'not_applicable')" ) # Result 2: early_phase_1 conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, trial_id, failure_category, " " confidence_tier, source_db, source_record_id, extraction_method, " " highest_phase_reached) " "VALUES (1, 1, 2, 'efficacy', 'bronze', 'aact', 'P002', " "'nlp_classified', 'early_phase_1')" ) conn.commit() refresh_all_ct_pairs(conn) conn.commit() row = conn.execute( "SELECT highest_phase_reached FROM intervention_condition_pairs " "WHERE intervention_id = 1 AND condition_id = 1" ).fetchone() # early_phase_1 (rank 2) should beat not_applicable (rank 1) assert row[0] == "early_phase_1" finally: conn.close() class TestMigration002Fixes: """Test migration 002 schema additions.""" def test_unique_constraint_prevents_duplicates(self, ct_db): """Same (intervention, condition, trial, source, record) should fail.""" conn = get_connection(ct_db) try: conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'DrugU')" ) conn.execute( "INSERT INTO conditions (condition_name) VALUES ('DiseaseU')" ) conn.commit() conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method) " "VALUES (1, 1, 'efficacy', 'gold', 'aact', 'U001', 'database_direct')" ) conn.commit() with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method) " "VALUES (1, 1, 'safety', 'silver', 'aact', 'U001', 'database_direct')" ) finally: conn.close() def test_unique_constraint_allows_different_sources(self, ct_db): """Same intervention+condition but different source_record_id is OK.""" conn = get_connection(ct_db) try: conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'DrugV')" ) conn.execute( "INSERT INTO conditions (condition_name) VALUES ('DiseaseV')" ) conn.commit() conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method) " "VALUES (1, 1, 'efficacy', 'gold', 'aact', 'V001', 'database_direct')" ) conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method) " "VALUES (1, 1, 'efficacy', 'silver', 'aact', 'V002', 'database_direct')" ) conn.commit() count = conn.execute( "SELECT COUNT(*) FROM trial_failure_results" ).fetchone()[0] assert count == 2 finally: conn.close() def test_interventions_has_inchikey_columns(self, ct_db): conn = get_connection(ct_db) try: conn.execute( "INSERT INTO interventions " "(intervention_type, intervention_name, inchikey, inchikey_connectivity) " "VALUES ('drug', 'InChITest', 'XLYOFNOQVPJJNP-UHFFFAOYSA-N', " "'XLYOFNOQVPJJNP')" ) conn.commit() row = conn.execute( "SELECT inchikey, inchikey_connectivity FROM interventions " "WHERE intervention_name = 'InChITest'" ).fetchone() assert row[0] == "XLYOFNOQVPJJNP-UHFFFAOYSA-N" assert row[1] == "XLYOFNOQVPJJNP" finally: conn.close() def test_interventions_molecular_type_check(self, ct_db): conn = get_connection(ct_db) try: # Valid molecular_type conn.execute( "INSERT INTO interventions " "(intervention_type, intervention_name, molecular_type) " "VALUES ('drug', 'SmallMol', 'small_molecule')" ) conn.commit() # Invalid molecular_type with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO interventions " "(intervention_type, intervention_name, molecular_type) " "VALUES ('drug', 'Bad', 'invalid_type')" ) finally: conn.close() def test_result_interpretation_check(self, ct_db): conn = get_connection(ct_db) try: conn.execute( "INSERT INTO interventions (intervention_type, intervention_name) " "VALUES ('drug', 'InterpDrug')" ) conn.execute( "INSERT INTO conditions (condition_name) VALUES ('InterpDisease')" ) conn.commit() # Valid interpretation conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method, result_interpretation) " "VALUES (1, 1, 'efficacy', 'gold', 'aact', 'I001', " "'database_direct', 'definitive_negative')" ) conn.commit() # Invalid interpretation with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO trial_failure_results " "(intervention_id, condition_id, failure_category, confidence_tier, " " source_db, source_record_id, extraction_method, result_interpretation) " "VALUES (1, 1, 'efficacy', 'gold', 'aact', 'I002', " "'database_direct', 'invalid_interp')" ) finally: conn.close() def test_termination_type_check(self, ct_db): conn = get_connection(ct_db) try: # Valid termination_type conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status, termination_type) " "VALUES ('clinicaltrials_gov', 'NCT900', 'Terminated', 'clinical_failure')" ) conn.commit() # Invalid termination_type with pytest.raises(sqlite3.IntegrityError): conn.execute( "INSERT INTO clinical_trials " "(source_db, source_trial_id, overall_status, termination_type) " "VALUES ('clinicaltrials_gov', 'NCT901', 'Terminated', 'invalid')" ) finally: conn.close()