TST Test database consistency

tests/test_database.py

@@ -0,0 +1,24 @@
+from argnorm import lib
+from argnorm import drug_categorization
+
+def test_databases():
+    ARO = lib.get_aro_ontology()
+
+    determinant_of_ab_resistance = ARO['ARO:3000000']
+    antibiotic_molecule = ARO['ARO:1000003']
+    assert determinant_of_ab_resistance.name == 'determinant of antibiotic resistance'
+    assert antibiotic_molecule.name == 'antibiotic molecule'
+
+    for database in ['argannot', 'deeparg', 'megares', 'ncbi', 'resfinderfg', 'sarg']:
+        db = lib.get_aro_mapping_table(database)
+        assert len(db.index) == len(set(db.index)), f'Duplicate gene names in {database}'
+        for ar in db['ARO'].dropna():
+            assert ar in ARO, f'ARO not found in the ontology: {ar}'
+            assert determinant_of_ab_resistance in ARO[ar].superclasses(), f'ARO not a determinant of antibiotic resistance: {ar}'
+            for d in drug_categorization.confers_resistance_to(ar):
+                assert d in ARO, f'ARO not found in the ontology: {d}'
+                assert antibiotic_molecule in ARO[d].superclasses(), f'ARO not an antibiotic molecule: {d}'
+                for dc in drug_categorization.drugs_to_drug_classes([d]):
+                    assert dc in ARO, f'ARO not found in the ontology: {dc}'
+                    assert antibiotic_molecule in  ARO[dc].superclasses(1), f'ARO term not an immediate child of antibiotic molecule: {dc}'
+