add and update tests

Author: florian-huber

tests/test_ann_index.py

@@ -0,0 +1,189 @@
+import io
+import json
+import sqlite3
+from typing import List, Tuple
+
+import numpy as np
+import pytest
+from matchms import Spectrum
+
+from ms2query.database import ANNIndex
+from ms2query.database.spectra_merging import ensure_merged_tables
+
+# --- small helpers for array <-> BLOB used in tests (mirrors the production helpers) ---
+
+def _ndarray_to_blob(arr: np.ndarray) -> bytes:
+    with io.BytesIO() as f:
+        np.save(f, arr, allow_pickle=False)
+        return f.getvalue()
+
+
+@pytest.fixture()
+def conn() -> sqlite3.Connection:
+    # In-memory DB for tests
+    return sqlite3.connect(":memory:")
+
+
+@pytest.fixture()
+def ann(conn) -> ANNIndex:
+    # Instantiate with dummy model path; we’ll monkeypatch load_model.
+    return ANNIndex(
+        conn=conn,
+        model_path="dummy_model.pt",
+        faiss_metric="ip",
+        faiss_factory=None,
+        normalize_embeddings=True,
+    )
+
+
+def test_ensure_schema_creates_tables(ann: ANNIndex):
+    """Schema should be created with all required columns."""
+    ann.ensure_schema()
+    cur = ann.conn.cursor()
+    # Check both tables exist
+    cur.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='merged_spectra';")
+    assert cur.fetchone() is not None
+    cur.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='merged_embeddings';")
+    assert cur.fetchone() is not None
+
+    # Check a few critical columns exist
+    cur.execute("PRAGMA table_info('merged_spectra');")
+    cols = {row[1] for row in cur.fetchall()}
+    for required in ("merged_id", "comp_id", "precursor_mz", "mz", "intensities", "num_merged"):
+        assert required in cols
+
+
+def _insert_synthetic_merged_rows(conn: sqlite3.Connection) -> Tuple[int, int]:
+    """
+    Insert two tiny merged_spectra rows with minimal viable metadata.
+    Returns their merged_ids (sqlite autoincrement).
+    """
+    cur = conn.cursor()
+    ensure_merged_tables(conn)
+
+    # Synthetic peaks
+    mz1 = np.array([100.0, 150.0, 200.0], dtype=np.float64)
+    it1 = np.array([0.2, 0.3, 0.5], dtype=np.float32)
+
+    mz2 = np.array([101.0, 151.0, 201.0], dtype=np.float64)
+    it2 = np.array([0.4, 0.1, 0.5], dtype=np.float32)
+
+    base_cols = (
+        "comp_id, ionmode, charge, precursor_mz, smiles, inchikey, inchi, name, "
+        "instrument_type, adduct, collision_energy, num_merged, source_spec_ids, mz, intensities"
+    )
+    q = f"INSERT INTO merged_spectra ({base_cols}) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?);"
+
+    cur.execute(
+        q,
+        (
+            "C1", "positive", 1, 300.123, "C(CO)O", "AAAA-BBBB-CCCC", "InChI=1S/...", "Compound A",
+            "QTOF", "[M+H]+", "NCE 20", 3, json.dumps([11, 12, 13]),
+            sqlite3.Binary(_ndarray_to_blob(mz1)), sqlite3.Binary(_ndarray_to_blob(it1))
+        ),
+    )
+    id1 = cur.lastrowid
+
+    cur.execute(
+        q,
+        (
+            "C2", "positive", 1, 450.5, "CCN(CC)CC", "XXXX-YYYY-ZZZZ", "InChI=1S/...", "Compound B",
+            "Orbitrap", "[M+H]+", "NCE 25", 2, json.dumps([21, 22]),
+            sqlite3.Binary(_ndarray_to_blob(mz2)), sqlite3.Binary(_ndarray_to_blob(it2))
+        ),
+    )
+    id2 = cur.lastrowid
+
+    conn.commit()
+    return id1, id2
+
+
+def test_compute_embeddings_inserts_rows(ann: ANNIndex, monkeypatch):
+    """Embeddings should be computed and written; rerun with only_missing yields 0 new rows."""
+    id1, id2 = _insert_synthetic_merged_rows(ann.conn)
+
+    # Monkeypatch model loading and embedding to be deterministic & light.
+    class _DummyModel:
+        pass
+
+    def fake_load_model(_path):
+        return _DummyModel()
+
+    def fake_compute_embedding_array(model, specs: List[Spectrum]) -> np.ndarray:
+        # simple deterministic embedding: [precursor_mz, charge, sum(intens), len(peaks)]
+        out = []
+        for s in specs:
+            pmz = float(s.metadata["precursor_mz"])
+            charge = float(s.metadata.get("charge") or 0)
+            intens_sum = float(np.sum(s.peaks.intensities))
+            n_peaks = float(len(s.peaks.mz))
+            out.append([pmz, charge, intens_sum, n_peaks])
+        return np.asarray(out, dtype=np.float32)
+
+    monkeypatch.setattr("ms2query.database.ann_index.load_model", fake_load_model)
+    monkeypatch.setattr("ms2query.database.ann_index.compute_embedding_array", fake_compute_embedding_array)
+
+    inserted = ann.compute_embeddings_to_sqlite(batch_rows=64, only_missing=True)
+    assert inserted == 2
+
+    # Confirm rows exist
+    cur = ann.conn.cursor()
+    cur.execute("SELECT COUNT(1) FROM merged_embeddings;")
+    assert cur.fetchone()[0] == 2
+
+    # Re-run with only_missing: should insert 0
+    inserted2 = ann.compute_embeddings_to_sqlite(batch_rows=64, only_missing=True)
+    assert inserted2 == 0
+
+
+def test_build_index_and_query(ann: ANNIndex, monkeypatch):
+    """Build index from stored embeddings and query it; top-1 should be the intended nearest."""
+    id1, id2 = _insert_synthetic_merged_rows(ann.conn)
+
+    # Same monkeypatch as previous test (model + embeddings)
+    class _DummyModel:
+        pass
+
+    def fake_load_model(_path):
+        return _DummyModel()
+
+    def fake_compute_embedding_array(model, specs: List[Spectrum]) -> np.ndarray:
+        # Embedding consistent with test_compute_embeddings
+        out = []
+        for s in specs:
+            pmz = float(s.metadata["precursor_mz"])
+            charge = float(s.metadata.get("charge") or 0)
+            intens_sum = float(np.sum(s.peaks.intensities))
+            n_peaks = float(len(s.peaks.mz))
+            out.append([pmz, charge, intens_sum, n_peaks])
+        return np.asarray(out, dtype=np.float32)
+
+    monkeypatch.setattr("ms2query.database.ann_index.load_model", fake_load_model)
+    monkeypatch.setattr("ms2query.database.ann_index.compute_embedding_array", fake_compute_embedding_array)
+
+    # Compute embeddings
+    ann.compute_embeddings_to_sqlite(batch_rows=64, only_missing=False)
+
+    # Build FAISS index
+    index = ann.build_index()
+    assert index.ntotal == 2
+
+    # Prepare a query spectrum that should be closest to the 2nd row (precursor_mz=450.5)
+    q_mz = np.array([100.0, 200.0], dtype=np.float32)
+    q_it = np.array([0.5, 0.5], dtype=np.float32)
+    q_spec = Spectrum(mz=q_mz, intensities=q_it, metadata={"precursor_mz": 450.5, "ionmode": "positive", "charge": 1})
+
+    # Query
+    results = ann.query(q_spec, k=2, include_metadata=True, as_dataframe=True)
+    assert isinstance(results, list) and len(results) == 1
+    df = results[0]
+    assert {"rank", "merged_id", "score", "distance", "comp_id", "name"}.issubset(df.columns)
+
+    # Top-1 hit should be the row with precursor_mz=450.5 (id2)
+    top1 = df.iloc[0]
+    assert int(top1["merged_id"]) == id2
+    assert top1["comp_id"] == "C2"
+    assert top1["name"] == "Compound B"
+
+    # Scores should be non-increasing by rank
+    assert np.all(df["score"].values[:-1] >= df["score"].values[1:])

tests/test_compound_database.py

@@ -6,7 +6,7 @@
 import pytest
 
 # >>> adjust to your package/module path
-from ms2query.compound_database import (
+from ms2query.database.compound_database import (
     CompoundDatabase,
     SpecToCompoundMap,
     map_from_spectraldb_metadata,