from django.test import TestCase from epdb.logic import PackageManager from epdb.models import Compound, User, Reaction class CopyTest(TestCase): fixtures = ["test_fixtures.jsonl.gz"] @classmethod def setUpClass(cls): super(CopyTest, cls).setUpClass() cls.user = User.objects.get(username="anonymous") cls.package = PackageManager.create_package(cls.user, "Source Package", "No Desc") cls.AFOXOLANER = Compound.create( cls.package, smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C4=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F", name="Afoxolaner", description="Test compound for copying", ) cls.FOUR_NITROBENZOIC_ACID = Compound.create( cls.package, smiles="[O-][N+](=O)c1ccc(C(=O)[O-])cc1", # Normalized: O=C(O)C1=CC=C([N+](=O)[O-])C=C1', name="Test Compound", description="Compound with multiple structures", ) cls.ETHANOL = Compound.create( cls.package, smiles="CCO", name="Ethanol", description="Simple alcohol" ) cls.target_package = PackageManager.create_package(cls.user, "Target Package", "No Desc") cls.reaction_educt = Compound.create( cls.package, smiles="C(CCl)Cl", name="1,2-Dichloroethane", description="Eawag BBD compound c0001", ).default_structure cls.reaction_product = Compound.create( cls.package, smiles="C(CO)Cl", name="2-Chloroethanol", description="Eawag BBD compound c0005", ).default_structure cls.REACTION = Reaction.create( package=cls.package, name="Eawag BBD reaction r0001", educts=[cls.reaction_educt], products=[cls.reaction_product], multi_step=False, ) def test_compound_copy_basic(self): """Test basic compound copying functionality""" mapping = dict() copied_compound = self.AFOXOLANER.copy(self.target_package, mapping) self.assertNotEqual(self.AFOXOLANER.uuid, copied_compound.uuid) self.assertEqual(self.AFOXOLANER.name, copied_compound.name) self.assertEqual(self.AFOXOLANER.description, copied_compound.description) self.assertEqual(copied_compound.package, self.target_package) self.assertEqual(self.AFOXOLANER.package, self.package) self.assertEqual( self.AFOXOLANER.default_structure.smiles, copied_compound.default_structure.smiles ) def test_compound_copy_with_multiple_structures(self): """Test copying a compound with multiple structures""" original_structure_count = self.FOUR_NITROBENZOIC_ACID.structures.count() mapping = dict() # Copy the compound copied_compound = self.FOUR_NITROBENZOIC_ACID.copy(self.target_package, mapping) # Verify all structures were copied self.assertEqual(copied_compound.structures.count(), original_structure_count) # Verify default_structure is properly set self.assertIsNotNone(copied_compound.default_structure) self.assertEqual( copied_compound.default_structure.smiles, self.FOUR_NITROBENZOIC_ACID.default_structure.smiles, ) def test_compound_copy_preserves_aliases(self): """Test that compound copying preserves aliases""" # Create a compound and add aliases original_compound = self.ETHANOL # Add aliases if the method exists if hasattr(original_compound, "add_alias"): original_compound.add_alias("Ethyl alcohol") original_compound.add_alias("Grain alcohol") mapping = dict() copied_compound = original_compound.copy(self.target_package, mapping) # Verify aliases were copied if they exist if hasattr(original_compound, "aliases") and hasattr(copied_compound, "aliases"): original_aliases = original_compound.aliases copied_aliases = copied_compound.aliases self.assertEqual(original_aliases, copied_aliases) def test_compound_copy_preserves_external_identifiers(self): """Test that external identifiers are preserved during copying""" original_compound = self.ETHANOL # Add external identifiers if the methods exist if hasattr(original_compound, "add_cas_number"): original_compound.add_cas_number("64-17-5") if hasattr(original_compound, "add_pubchem_compound_id"): original_compound.add_pubchem_compound_id("702") mapping = dict() copied_compound = original_compound.copy(self.target_package, mapping) # Verify external identifiers were copied original_ext_ids = original_compound.external_identifiers.all() copied_ext_ids = copied_compound.external_identifiers.all() self.assertEqual(original_ext_ids.count(), copied_ext_ids.count()) # Check that identifier values match original_values = set(ext_id.identifier_value for ext_id in original_ext_ids) copied_values = set(ext_id.identifier_value for ext_id in copied_ext_ids) self.assertEqual(original_values, copied_values) def test_compound_copy_structure_properties(self): """Test that structure properties are properly copied""" original_compound = self.ETHANOL mapping = dict() copied_compound = original_compound.copy(self.target_package, mapping) # Verify structure properties original_structure = original_compound.default_structure copied_structure = copied_compound.default_structure self.assertEqual(original_structure.smiles, copied_structure.smiles) self.assertEqual(original_structure.canonical_smiles, copied_structure.canonical_smiles) self.assertEqual(original_structure.inchikey, copied_structure.inchikey) self.assertEqual( original_structure.normalized_structure, copied_structure.normalized_structure ) # Verify they are different objects self.assertNotEqual(original_structure.uuid, copied_structure.uuid) self.assertEqual(copied_structure.compound, copied_compound) def test_reaction_copy_basic(self): """Test basic reaction copying functionality""" mapping = dict() copied_reaction = self.REACTION.copy(self.target_package, mapping) self.assertNotEqual(self.REACTION.uuid, copied_reaction.uuid) self.assertEqual(self.REACTION.name, copied_reaction.name) self.assertEqual(self.REACTION.description, copied_reaction.description) self.assertEqual(self.REACTION.multi_step, copied_reaction.multi_step) self.assertEqual(copied_reaction.package, self.target_package) self.assertEqual(self.REACTION.package, self.package) def test_reaction_copy_structures(self): """Test basic reaction copying functionality""" mapping = dict() copied_reaction = self.REACTION.copy(self.target_package, mapping) for orig_educt, copy_educt in zip(self.REACTION.educts.all(), copied_reaction.educts.all()): self.assertNotEqual(orig_educt.uuid, copy_educt.uuid) self.assertEqual(orig_educt.name, copy_educt.name) self.assertEqual(orig_educt.description, copy_educt.description) self.assertEqual(copy_educt.compound.package, self.target_package) self.assertEqual(orig_educt.compound.package, self.package) self.assertEqual(orig_educt.smiles, copy_educt.smiles) for orig_product, copy_product in zip( self.REACTION.products.all(), copied_reaction.products.all() ): self.assertNotEqual(orig_product.uuid, copy_product.uuid) self.assertEqual(orig_product.name, copy_product.name) self.assertEqual(orig_product.description, copy_product.description) self.assertEqual(copy_product.compound.package, self.target_package) self.assertEqual(orig_product.compound.package, self.package) self.assertEqual(orig_product.smiles, copy_product.smiles)