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Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
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File size: 5,556 Bytes
6d1bbc7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 | """Tests for NegBioDB database creation and migration runner."""
import sqlite3
from pathlib import Path
import pytest
from negbiodb.db import connect, create_database, get_applied_versions, run_migrations
MIGRATIONS_DIR = Path(__file__).resolve().parent.parent / "migrations"
EXPECTED_TABLES = {
"compounds",
"targets",
"target_variants",
"assays",
"negative_results",
"dti_context",
"compound_target_pairs",
"split_definitions",
"split_assignments",
"dataset_versions",
"schema_migrations",
}
@pytest.fixture
def db_path(tmp_path):
return tmp_path / "test_negbiodb.db"
@pytest.fixture
def migrated_db(db_path):
create_database(db_path, MIGRATIONS_DIR)
return db_path
class TestMigrationRunner:
def test_creates_all_tables(self, migrated_db):
with connect(migrated_db) as conn:
rows = conn.execute(
"SELECT name FROM sqlite_master WHERE type='table' "
"AND name NOT LIKE 'sqlite_%'"
).fetchall()
tables = {row[0] for row in rows}
assert tables == EXPECTED_TABLES
def test_idempotent(self, migrated_db):
applied = run_migrations(migrated_db, MIGRATIONS_DIR)
assert applied == []
with connect(migrated_db) as conn:
count = conn.execute(
"SELECT COUNT(*) FROM schema_migrations"
).fetchone()[0]
assert count == 2
def test_schema_migrations_records_version(self, migrated_db):
with connect(migrated_db) as conn:
versions = get_applied_versions(conn)
assert "001" in versions
assert "002" in versions
def test_returns_applied_versions(self, db_path):
applied = run_migrations(db_path, MIGRATIONS_DIR)
assert applied == ["001", "002"]
class TestForeignKeys:
def test_fk_enforcement(self, migrated_db):
with connect(migrated_db) as conn:
with pytest.raises(sqlite3.IntegrityError):
conn.execute(
"INSERT INTO negative_results "
"(compound_id, target_id, result_type, confidence_tier, "
" source_db, source_record_id, extraction_method) "
"VALUES (99999, 99999, 'hard_negative', 'gold', "
" 'chembl', 'TEST001', 'database_direct')"
)
class TestUniqueConstraints:
def _insert_compound(self, conn, smiles="CCO",
inchikey="LFQSCWFLJHTTHZ-UHFFFAOYSA-N"):
conn.execute(
"INSERT INTO compounds (canonical_smiles, inchikey, "
"inchikey_connectivity) VALUES (?, ?, ?)",
(smiles, inchikey, inchikey[:14]),
)
return conn.execute("SELECT last_insert_rowid()").fetchone()[0]
def _insert_target(self, conn, accession="P00533"):
conn.execute(
"INSERT INTO targets (uniprot_accession) VALUES (?)",
(accession,),
)
return conn.execute("SELECT last_insert_rowid()").fetchone()[0]
def test_duplicate_source_record_rejected(self, migrated_db):
"""NULL assay_id duplicates should be caught by COALESCE index."""
with connect(migrated_db) as conn:
cid = self._insert_compound(conn)
tid = self._insert_target(conn)
conn.commit()
conn.execute(
"INSERT INTO negative_results "
"(compound_id, target_id, assay_id, result_type, confidence_tier, "
" source_db, source_record_id, extraction_method) "
"VALUES (?, ?, NULL, 'hard_negative', 'gold', "
" 'chembl', 'REC001', 'database_direct')",
(cid, tid),
)
conn.commit()
with pytest.raises(sqlite3.IntegrityError):
conn.execute(
"INSERT INTO negative_results "
"(compound_id, target_id, assay_id, result_type, confidence_tier, "
" source_db, source_record_id, extraction_method) "
"VALUES (?, ?, NULL, 'hard_negative', 'gold', "
" 'chembl', 'REC001', 'database_direct')",
(cid, tid),
)
def test_different_source_records_accepted(self, migrated_db):
with connect(migrated_db) as conn:
cid = self._insert_compound(conn)
tid = self._insert_target(conn)
conn.commit()
for rec_id in ["REC001", "REC002"]:
conn.execute(
"INSERT INTO negative_results "
"(compound_id, target_id, assay_id, result_type, confidence_tier, "
" source_db, source_record_id, extraction_method) "
"VALUES (?, ?, NULL, 'hard_negative', 'gold', "
" 'chembl', ?, 'database_direct')",
(cid, tid, rec_id),
)
conn.commit()
count = conn.execute(
"SELECT COUNT(*) FROM negative_results"
).fetchone()[0]
assert count == 2
class TestConnectionPragmas:
def test_wal_mode(self, migrated_db):
with connect(migrated_db) as conn:
mode = conn.execute("PRAGMA journal_mode").fetchone()[0]
assert mode == "wal"
def test_foreign_keys_on(self, migrated_db):
with connect(migrated_db) as conn:
fk = conn.execute("PRAGMA foreign_keys").fetchone()[0]
assert fk == 1
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