Add first test run ms2query

Author: niekdejonge

tests/test_run_ms2query.py

@@ -0,0 +1,34 @@
+from ms2query.benchmarking.AnnotatedSpectrumSet import AnnotatedSpectrumSet
+from ms2query.benchmarking.Fingerprints import Fingerprints
+from ms2query.benchmarking.TopKTanimotoScores import TopKTanimotoScores
+from ms2query.run_ms2query import extract_metadata_from_library, run_ms2query
+from tests.helper_functions import create_test_spectra, ms2deepscore_model
+
+
+def test_run_ms2query():
+    model = ms2deepscore_model()
+    library_spectra = AnnotatedSpectrumSet.create_spectrum_set(create_test_spectra(nr_of_inchikeys=7))
+    test_spectra = AnnotatedSpectrumSet.create_spectrum_set(create_test_spectra(1, nr_of_inchikeys=3))
+    library_spectra.add_embeddings(model)
+    test_spectra.add_embeddings(model)
+    fingerprints = Fingerprints.from_spectrum_set(library_spectra, "daylight", 100)
+    top_k_tanimoto_scores = TopKTanimotoScores.calculate_from_fingerprints(fingerprints, fingerprints, 3)
+    spectrum_indices_per_inchikey = library_spectra.spectrum_indices_per_inchikey
+    metadata_library = extract_metadata_from_library(
+        library_spectra,
+        [
+            "precursor_mz",
+            "collision_energy",
+            "compound_name",
+            "smiles",
+            "inchikey",
+        ],
+    )
+    results = run_ms2query(
+        test_spectra.embeddings,
+        library_spectra.embeddings,
+        metadata_library,
+        spectrum_indices_per_inchikey,
+        top_k_tanimoto_scores,
+    )
+    print(results)