forked from enviPath/enviPy
[Chore] Linted Files (#150)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#150
This commit is contained in:
@ -1,6 +1,5 @@
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from django.test import TestCase
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from django.test import TestCase
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from epdb.logic import PackageManager
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from epdb.models import Compound, User, Reaction
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@ -12,50 +11,47 @@ class CopyTest(TestCase):
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@classmethod
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def setUpClass(cls):
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super(CopyTest, cls).setUpClass()
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cls.user = User.objects.get(username='anonymous')
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cls.package = PackageManager.create_package(cls.user, 'Source Package', 'No Desc')
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cls.user = User.objects.get(username="anonymous")
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cls.package = PackageManager.create_package(cls.user, "Source Package", "No Desc")
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cls.AFOXOLANER = Compound.create(
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cls.package,
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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',
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name='Afoxolaner',
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description='Test compound for copying'
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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",
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name="Afoxolaner",
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description="Test compound for copying",
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)
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cls.FOUR_NITROBENZOIC_ACID = Compound.create(
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cls.package,
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smiles='[O-][N+](=O)c1ccc(C(=O)[O-])cc1', # Normalized: O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
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name='Test Compound',
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description='Compound with multiple structures'
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smiles="[O-][N+](=O)c1ccc(C(=O)[O-])cc1", # Normalized: O=C(O)C1=CC=C([N+](=O)[O-])C=C1',
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name="Test Compound",
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description="Compound with multiple structures",
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)
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cls.ETHANOL = Compound.create(
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cls.package,
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smiles='CCO',
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name='Ethanol',
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description='Simple alcohol'
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cls.package, smiles="CCO", name="Ethanol", description="Simple alcohol"
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)
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cls.target_package = PackageManager.create_package(cls.user, 'Target Package', 'No Desc')
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cls.target_package = PackageManager.create_package(cls.user, "Target Package", "No Desc")
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cls.reaction_educt = Compound.create(
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cls.package,
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smiles='C(CCl)Cl',
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name='1,2-Dichloroethane',
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description='Eawag BBD compound c0001'
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smiles="C(CCl)Cl",
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name="1,2-Dichloroethane",
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description="Eawag BBD compound c0001",
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).default_structure
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cls.reaction_product = Compound.create(
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cls.package,
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smiles='C(CO)Cl',
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name='2-Chloroethanol',
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description='Eawag BBD compound c0005'
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smiles="C(CO)Cl",
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name="2-Chloroethanol",
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description="Eawag BBD compound c0005",
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).default_structure
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cls.REACTION = Reaction.create(
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package=cls.package,
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name='Eawag BBD reaction r0001',
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name="Eawag BBD reaction r0001",
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educts=[cls.reaction_educt],
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products=[cls.reaction_product],
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multi_step=False
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multi_step=False,
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)
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def test_compound_copy_basic(self):
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@ -68,7 +64,9 @@ class CopyTest(TestCase):
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self.assertEqual(self.AFOXOLANER.description, copied_compound.description)
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self.assertEqual(copied_compound.package, self.target_package)
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self.assertEqual(self.AFOXOLANER.package, self.package)
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self.assertEqual(self.AFOXOLANER.default_structure.smiles, copied_compound.default_structure.smiles)
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self.assertEqual(
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self.AFOXOLANER.default_structure.smiles, copied_compound.default_structure.smiles
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)
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def test_compound_copy_with_multiple_structures(self):
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"""Test copying a compound with multiple structures"""
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@ -86,7 +84,7 @@ class CopyTest(TestCase):
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self.assertIsNotNone(copied_compound.default_structure)
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self.assertEqual(
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copied_compound.default_structure.smiles,
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self.FOUR_NITROBENZOIC_ACID.default_structure.smiles
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self.FOUR_NITROBENZOIC_ACID.default_structure.smiles,
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)
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def test_compound_copy_preserves_aliases(self):
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@ -95,15 +93,15 @@ class CopyTest(TestCase):
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original_compound = self.ETHANOL
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# Add aliases if the method exists
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if hasattr(original_compound, 'add_alias'):
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original_compound.add_alias('Ethyl alcohol')
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original_compound.add_alias('Grain alcohol')
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if hasattr(original_compound, "add_alias"):
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original_compound.add_alias("Ethyl alcohol")
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original_compound.add_alias("Grain alcohol")
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mapping = dict()
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copied_compound = original_compound.copy(self.target_package, mapping)
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# Verify aliases were copied if they exist
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if hasattr(original_compound, 'aliases') and hasattr(copied_compound, 'aliases'):
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if hasattr(original_compound, "aliases") and hasattr(copied_compound, "aliases"):
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original_aliases = original_compound.aliases
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copied_aliases = copied_compound.aliases
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self.assertEqual(original_aliases, copied_aliases)
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@ -113,10 +111,10 @@ class CopyTest(TestCase):
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original_compound = self.ETHANOL
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# Add external identifiers if the methods exist
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if hasattr(original_compound, 'add_cas_number'):
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original_compound.add_cas_number('64-17-5')
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if hasattr(original_compound, 'add_pubchem_compound_id'):
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original_compound.add_pubchem_compound_id('702')
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if hasattr(original_compound, "add_cas_number"):
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original_compound.add_cas_number("64-17-5")
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if hasattr(original_compound, "add_pubchem_compound_id"):
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original_compound.add_pubchem_compound_id("702")
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mapping = dict()
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copied_compound = original_compound.copy(self.target_package, mapping)
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@ -146,7 +144,9 @@ class CopyTest(TestCase):
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self.assertEqual(original_structure.smiles, copied_structure.smiles)
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self.assertEqual(original_structure.canonical_smiles, copied_structure.canonical_smiles)
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self.assertEqual(original_structure.inchikey, copied_structure.inchikey)
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self.assertEqual(original_structure.normalized_structure, copied_structure.normalized_structure)
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self.assertEqual(
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original_structure.normalized_structure, copied_structure.normalized_structure
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)
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# Verify they are different objects
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self.assertNotEqual(original_structure.uuid, copied_structure.uuid)
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@ -177,7 +177,9 @@ class CopyTest(TestCase):
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self.assertEqual(orig_educt.compound.package, self.package)
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self.assertEqual(orig_educt.smiles, copy_educt.smiles)
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for orig_product, copy_product in zip(self.REACTION.products.all(), copied_reaction.products.all()):
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for orig_product, copy_product in zip(
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self.REACTION.products.all(), copied_reaction.products.all()
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):
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self.assertNotEqual(orig_product.uuid, copy_product.uuid)
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self.assertEqual(orig_product.name, copy_product.name)
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self.assertEqual(orig_product.description, copy_product.description)
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