enviPy-bayer/tests/test_simpleambitrule.py

from unittest.mock import patch, MagicMock, PropertyMock

from django.test import TestCase

from epdb.logic import PackageManager
from epdb.models import User, SimpleAmbitRule


class SimpleAmbitRuleTest(TestCase):
    fixtures = ["test_fixtures.jsonl.gz"]

    @classmethod
    def setUpClass(cls):
        super(SimpleAmbitRuleTest, cls).setUpClass()
        cls.user = User.objects.get(username='anonymous')
        cls.package = PackageManager.create_package(cls.user, 'Simple Ambit Rule Test Package',
                                                    'Test Package for SimpleAmbitRule')

    def test_create_basic_rule(self):
        """Test creating a basic SimpleAmbitRule with minimal parameters."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'

        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks
        )

        self.assertIsInstance(rule, SimpleAmbitRule)
        self.assertEqual(rule.smirks, smirks)
        self.assertEqual(rule.package, self.package)
        self.assertRegex(rule.name, r'Rule \d+')
        self.assertEqual(rule.description, 'no description')
        self.assertIsNone(rule.reactant_filter_smarts)
        self.assertIsNone(rule.product_filter_smarts)

    def test_create_with_all_parameters(self):
        """Test creating SimpleAmbitRule with all parameters."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
        name = 'Test Rule'
        description = 'A test biotransformation rule'
        reactant_filter = '[CH2X4]'
        product_filter = '[OH]'

        rule = SimpleAmbitRule.create(
            package=self.package,
            name=name,
            description=description,
            smirks=smirks,
            reactant_filter_smarts=reactant_filter,
            product_filter_smarts=product_filter
        )

        self.assertEqual(rule.name, name)
        self.assertEqual(rule.description, description)
        self.assertEqual(rule.smirks, smirks)
        self.assertEqual(rule.reactant_filter_smarts, reactant_filter)
        self.assertEqual(rule.product_filter_smarts, product_filter)

    def test_smirks_required(self):
        """Test that SMIRKS is required for rule creation."""
        with self.assertRaises(ValueError) as cm:
            SimpleAmbitRule.create(package=self.package, smirks=None)
        self.assertIn('SMIRKS is required', str(cm.exception))

        with self.assertRaises(ValueError) as cm:
            SimpleAmbitRule.create(package=self.package, smirks='')
        self.assertIn('SMIRKS is required', str(cm.exception))

        with self.assertRaises(ValueError) as cm:
            SimpleAmbitRule.create(package=self.package, smirks='   ')
        self.assertIn('SMIRKS is required', str(cm.exception))

    @patch('epdb.models.FormatConverter.is_valid_smirks')
    def test_invalid_smirks_validation(self, mock_is_valid):
        """Test validation of SMIRKS format."""
        mock_is_valid.return_value = False

        invalid_smirks = 'invalid_smirks_string'
        with self.assertRaises(ValueError) as cm:
            SimpleAmbitRule.create(
                package=self.package,
                smirks=invalid_smirks
            )

        self.assertIn(f'SMIRKS "{invalid_smirks}" is invalid', str(cm.exception))
        mock_is_valid.assert_called_once_with(invalid_smirks)

    def test_smirks_trimming(self):
        """Test that SMIRKS strings are trimmed during creation."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
        smirks_with_whitespace = f'   {smirks}   '

        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks_with_whitespace
        )

        self.assertEqual(rule.smirks, smirks)

    def test_empty_name_and_description_handling(self):
        """Test that empty name and description are handled appropriately."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'

        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks,
            name='',
            description='   '
        )

        self.assertRegex(rule.name, r'Rule \d+')
        self.assertEqual(rule.description, 'no description')

    def test_deduplication_basic(self):
        """Test that identical rules are deduplicated."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'

        rule1 = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks,
            name='Rule 1'
        )

        rule2 = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks,
            name='Rule 2'  # Different name, but same SMIRKS
        )

        self.assertEqual(rule1.pk, rule2.pk)
        self.assertEqual(SimpleAmbitRule.objects.filter(package=self.package, smirks=smirks).count(), 1)

    def test_deduplication_with_filters(self):
        """Test deduplication with filter SMARTS."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
        reactant_filter = '[CH2X4]'
        product_filter = '[OH]'

        rule1 = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks,
            reactant_filter_smarts=reactant_filter,
            product_filter_smarts=product_filter
        )

        rule2 = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks,
            reactant_filter_smarts=reactant_filter,
            product_filter_smarts=product_filter
        )

        self.assertEqual(rule1.pk, rule2.pk)

    def test_no_deduplication_different_filters(self):
        """Test that rules with different filters are not deduplicated."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'

        rule1 = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks,
            reactant_filter_smarts='[CH2X4]'
        )

        rule2 = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks,
            reactant_filter_smarts='[CH3X4]'
        )

        self.assertNotEqual(rule1.pk, rule2.pk)
        self.assertEqual(SimpleAmbitRule.objects.filter(package=self.package, smirks=smirks).count(), 2)

    def test_filter_smarts_trimming(self):
        """Test that filter SMARTS are trimmed and handled correctly."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'

        # Test with whitespace-only filters (should be treated as None)
        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks,
            reactant_filter_smarts='   ',
            product_filter_smarts='   '
        )

        self.assertIsNone(rule.reactant_filter_smarts)
        self.assertIsNone(rule.product_filter_smarts)

    def test_url_property(self):
        """Test the URL property generation."""
        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks='[H:1][C:2]>>[H:1][O:2]'
        )

        expected_url = f'{self.package.url}/simple-ambit-rule/{rule.uuid}'
        self.assertEqual(rule.url, expected_url)

    @patch('epdb.models.FormatConverter.apply')
    def test_apply_method(self, mock_apply):
        """Test the apply method delegates to FormatConverter."""
        mock_apply.return_value = ['product1', 'product2']

        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks='[H:1][C:2]>>[H:1][O:2]'
        )

        test_smiles = 'CCO'
        result = rule.apply(test_smiles)

        mock_apply.assert_called_once_with(test_smiles, rule.smirks)
        self.assertEqual(result, ['product1', 'product2'])

    def test_reactants_smarts_property(self):
        """Test reactants_smarts property extracts correct part of SMIRKS."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
        expected_reactants = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]'

        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks
        )

        self.assertEqual(rule.reactants_smarts, expected_reactants)

    def test_products_smarts_property(self):
        """Test products_smarts property extracts correct part of SMIRKS."""
        smirks = '[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'
        expected_products = '[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]'

        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks=smirks
        )

        self.assertEqual(rule.products_smarts, expected_products)

    @patch('epdb.models.Package.objects')
    def test_related_reactions_property(self, mock_package_objects):
        """Test related_reactions property returns correct queryset."""
        mock_qs = MagicMock()
        mock_package_objects.filter.return_value = mock_qs

        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks='[H:1][C:2]>>[H:1][O:2]'
        )

        # Instead of directly assigning, patch the property or use with patch.object
        with patch.object(type(rule), 'reaction_rule', new_callable=PropertyMock) as mock_reaction_rule:
            mock_reaction_rule.return_value.filter.return_value.order_by.return_value = ['reaction1', 'reaction2']

            result = rule.related_reactions

            mock_package_objects.filter.assert_called_once_with(reviewed=True)
            mock_reaction_rule.return_value.filter.assert_called_once_with(package__in=mock_qs)
            mock_reaction_rule.return_value.filter.return_value.order_by.assert_called_once_with('name')
            self.assertEqual(result, ['reaction1', 'reaction2'])

    @patch('epdb.models.Pathway.objects')
    @patch('epdb.models.Edge.objects')
    def test_related_pathways_property(self, mock_edge_objects, mock_pathway_objects):
        """Test related_pathways property returns correct queryset."""

        mock_related_reactions = ['reaction1', 'reaction2']

        with patch.object(SimpleAmbitRule, "related_reactions", new_callable=PropertyMock) as mock_prop:
            mock_prop.return_value = mock_related_reactions

            rule = SimpleAmbitRule.create(
                package=self.package,
                smirks='[H:1][C:2]>>[H:1][O:2]'
            )

            # Mock Edge objects query
            mock_edge_values = MagicMock()
            mock_edge_values.values.return_value = ['pathway_id1', 'pathway_id2']
            mock_edge_objects.filter.return_value = mock_edge_values

            # Mock Pathway objects query
            mock_pathway_qs = MagicMock()
            mock_pathway_objects.filter.return_value.order_by.return_value = mock_pathway_qs

            result = rule.related_pathways

            mock_edge_objects.filter.assert_called_once_with(edge_label__in=mock_related_reactions)
            mock_edge_values.values.assert_called_once_with('pathway_id')
            mock_pathway_objects.filter.assert_called_once()
            self.assertEqual(result, mock_pathway_qs)

    @patch('epdb.models.IndigoUtils.smirks_to_svg')
    def test_as_svg_property(self, mock_smirks_to_svg):
        """Test as_svg property calls IndigoUtils correctly."""
        mock_smirks_to_svg.return_value = '<svg>test_svg</svg>'

        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks='[H:1][C:2]>>[H:1][O:2]'
        )

        result = rule.as_svg
        mock_smirks_to_svg.assert_called_once_with(rule.smirks, True, width=800, height=400)
        self.assertEqual(result, '<svg>test_svg</svg>')

    def test_atomic_transaction(self):
        """Test that rule creation is atomic."""
        smirks = '[H:1][C:2]>>[H:1][O:2]'

        # This should work normally
        rule = SimpleAmbitRule.create(package=self.package, smirks=smirks)
        self.assertIsInstance(rule, SimpleAmbitRule)

        # Test transaction rollback on error
        with patch('epdb.models.SimpleAmbitRule.save', side_effect=Exception('Database error')):
            with self.assertRaises(Exception):
                SimpleAmbitRule.create(package=self.package, smirks='[H:3][C:4]>>[H:3][O:4]')

        # Verify no partial data was saved
        self.assertEqual(SimpleAmbitRule.objects.filter(package=self.package).count(), 1)

    def test_multiple_duplicate_warning(self):
        """Test logging when multiple duplicates are found."""
        smirks = '[H:1][C:2]>>[H:1][O:2]'

        # Create first rule
        rule1 = SimpleAmbitRule.create(package=self.package, smirks=smirks)

        # Manually create a duplicate to simulate the error condition
        rule2 = SimpleAmbitRule(package=self.package, smirks=smirks, name='Manual Rule')
        rule2.save()

        with patch('epdb.models.logger') as mock_logger:
            # This should find the existing rule and log an error about multiple matches
            result = SimpleAmbitRule.create(package=self.package, smirks=smirks)

            # Should return the first matching rule
            self.assertEqual(result.pk, rule1.pk)

            # Should log an error about multiple matches
            mock_logger.error.assert_called()
            self.assertIn('More than one rule matched', mock_logger.error.call_args[0][0])

    def test_model_fields(self):
        """Test model field properties."""
        rule = SimpleAmbitRule.create(
            package=self.package,
            smirks='[H:1][C:2]>>[H:1][O:2]',
            reactant_filter_smarts='[CH3]',
            product_filter_smarts='[OH]'
        )

        # Test field properties
        self.assertFalse(rule._meta.get_field('smirks').blank)
        self.assertFalse(rule._meta.get_field('smirks').null)
        self.assertTrue(rule._meta.get_field('reactant_filter_smarts').null)
        self.assertTrue(rule._meta.get_field('product_filter_smarts').null)

        # Test verbose names
        self.assertEqual(rule._meta.get_field('smirks').verbose_name, 'SMIRKS')
        self.assertEqual(rule._meta.get_field('reactant_filter_smarts').verbose_name, 'Reactant Filter SMARTS')
        self.assertEqual(rule._meta.get_field('product_filter_smarts').verbose_name, 'Product Filter SMARTS')