fix(ingestion): skip mark-deleted for schemas whose table listing failed

ingestion/src/metadata/ingestion/source/database/common_db_source.py

@@ -412,6 +412,15 @@ def get_tables_name_and_type(self) -> Optional[Iterable[Tuple[str, str]]]:  # no
         except Exception as err:
             logger.warning(f"Fetching tables names failed for schema {schema_name} due to - {err}")
             logger.debug(traceback.format_exc())
+            schema_fqn = fqn.build(
+                self.metadata,
+                entity_type=DatabaseSchema,
+                service_name=self.context.get().database_service,
+                database_name=self.context.get().database,
+                schema_name=schema_name,
+            )
+            if schema_fqn:
+                self.schemas_with_table_listing_errors.add(schema_fqn)
 
     @calculate_execution_time()
     def get_schema_definition(

ingestion/src/metadata/ingestion/source/database/database_service.py

@@ -215,6 +215,10 @@ class DatabaseServiceSource(TopologyRunnerMixin, Source, ABC):  # pylint: disabl
     stored_procedure_source_state: Set = set()  # noqa: RUF012, UP006
     database_entity_source_state: Set = set()  # noqa: RUF012, UP006
     schema_entity_source_state: Set = set()  # noqa: RUF012, UP006
+    # Schemas whose table listing raised an exception during ingestion.
+    # mark_deleted_tables must skip these to avoid wiping tables that exist
+    # but were simply unreachable due to a transient connectivity failure.
+    schemas_with_table_listing_errors: Set = set()  # noqa: RUF012, UP006
     # Big union of types we want to fetch dynamically
     service_connection: DatabaseConnection.model_fields["config"].annotation  # noqa: F821
 
@@ -707,6 +711,12 @@ def mark_tables_as_deleted(self):
             schema_fqn_list = self._get_filtered_schema_names(return_fqn=True, add_to_status=False)
 
             for schema_fqn in schema_fqn_list:
+                if schema_fqn in self.schemas_with_table_listing_errors:
+                    logger.warning(
+                        f"Skipping mark-deleted for schema [{schema_fqn}]: "
+                        "table listing failed during ingestion — tables may still exist"
+                    )
+                    continue
                 yield from delete_entity_from_source(
                     metadata=self.metadata,
                     entity_type=Table,

ingestion/tests/unit/topology/database/test_mark_deleted_tables_safety.py

@@ -0,0 +1,246 @@
+#  Copyright 2025 Collate
+#  Licensed under the Collate Community License, Version 1.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#  https://github.com/open-metadata/OpenMetadata/blob/main/ingestion/LICENSE
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+"""
+Tests for the mark-deleted safety guard introduced in issue #18187.
+
+The fix ensures that when table listing fails for a schema (e.g. due to a
+transient connectivity error), `mark_tables_as_deleted` skips that schema
+rather than wiping all of its tables from OpenMetadata.
+"""
+
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from metadata.ingestion.source.database.database_service import DatabaseServiceSource
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+HEALTHY_SCHEMA = "my_service.my_db.healthy_schema"
+FAILED_SCHEMA = "my_service.my_db.broken_schema"
+ANOTHER_HEALTHY_SCHEMA = "my_service.my_db.another_schema"
+
+
+def _make_source(schema_fqn_list: list, mark_deleted: bool = True) -> MagicMock:
+    """Return a MagicMock that delegates the real mark_tables_as_deleted."""
+    source = MagicMock(spec=DatabaseServiceSource)
+    source.mark_tables_as_deleted = DatabaseServiceSource.mark_tables_as_deleted.__get__(source)
+
+    ctx = MagicMock()
+    ctx.database = "my_db"
+    source.context.get.return_value = ctx
+
+    source.source_config.markDeletedTables = mark_deleted
+    source._get_filtered_schema_names.return_value = schema_fqn_list
+    source.schemas_with_table_listing_errors = set()
+    source.database_source_state = set()
+
+    return source
+
+
+# ---------------------------------------------------------------------------
+# Tests: mark_tables_as_deleted skips failed schemas
+# ---------------------------------------------------------------------------
+
+
+class TestMarkDeletedTablesSafety:
+    def test_no_failed_schemas_processes_all(self):
+        """When no schema had listing errors, delete_entity_from_source is called for each."""
+        source = _make_source([HEALTHY_SCHEMA, ANOTHER_HEALTHY_SCHEMA])
+
+        with patch(
+            "metadata.ingestion.source.database.database_service.delete_entity_from_source",
+            return_value=iter([]),
+        ) as mock_delete:
+            list(source.mark_tables_as_deleted())
+
+        assert mock_delete.call_count == 2
+        called_schemas = {call.kwargs["params"]["database"] for call in mock_delete.call_args_list}
+        assert called_schemas == {HEALTHY_SCHEMA, ANOTHER_HEALTHY_SCHEMA}
+
+    def test_failed_schema_is_skipped(self):
+        """A schema in schemas_with_table_listing_errors must never reach delete_entity_from_source."""
+        source = _make_source([HEALTHY_SCHEMA, FAILED_SCHEMA])
+        source.schemas_with_table_listing_errors.add(FAILED_SCHEMA)
+
+        with patch(
+            "metadata.ingestion.source.database.database_service.delete_entity_from_source",
+            return_value=iter([]),
+        ) as mock_delete:
+            list(source.mark_tables_as_deleted())
+
+        assert mock_delete.call_count == 1
+        assert mock_delete.call_args.kwargs["params"]["database"] == HEALTHY_SCHEMA
+
+    def test_all_failed_schemas_skips_all_deletes(self):
+        """If every schema failed listing, delete_entity_from_source is never called."""
+        source = _make_source([FAILED_SCHEMA])
+        source.schemas_with_table_listing_errors.add(FAILED_SCHEMA)
+
+        with patch(
+            "metadata.ingestion.source.database.database_service.delete_entity_from_source",
+            return_value=iter([]),
+        ) as mock_delete:
+            list(source.mark_tables_as_deleted())
+
+        mock_delete.assert_not_called()
+
+    def test_mark_deleted_false_skips_everything(self):
+        """When markDeletedTables is False, nothing runs regardless of error state."""
+        source = _make_source([HEALTHY_SCHEMA, FAILED_SCHEMA], mark_deleted=False)
+
+        with patch(
+            "metadata.ingestion.source.database.database_service.delete_entity_from_source",
+            return_value=iter([]),
+        ) as mock_delete:
+            list(source.mark_tables_as_deleted())
+
+        mock_delete.assert_not_called()
+
+    def test_multiple_failed_schemas_only_skips_those(self):
+        """Only the failed schemas are skipped; healthy ones still get processed."""
+        schemas = [HEALTHY_SCHEMA, FAILED_SCHEMA, ANOTHER_HEALTHY_SCHEMA]
+        source = _make_source(schemas)
+        source.schemas_with_table_listing_errors.add(FAILED_SCHEMA)
+
+        with patch(
+            "metadata.ingestion.source.database.database_service.delete_entity_from_source",
+            return_value=iter([]),
+        ) as mock_delete:
+            list(source.mark_tables_as_deleted())
+
+        assert mock_delete.call_count == 2
+        called_schemas = {call.kwargs["params"]["database"] for call in mock_delete.call_args_list}
+        assert called_schemas == {HEALTHY_SCHEMA, ANOTHER_HEALTHY_SCHEMA}
+        assert FAILED_SCHEMA not in called_schemas
+
+
+# ---------------------------------------------------------------------------
+# Tests: get_tables_name_and_type populates schemas_with_table_listing_errors
+# ---------------------------------------------------------------------------
+
+
+class TestGetTablesNameAndTypeErrorTracking:
+    def _make_common_source(self, schema_name: str, schema_fqn: str) -> MagicMock:
+        """Minimal mock for CommonDbSourceService.get_tables_name_and_type."""
+        from metadata.ingestion.source.database.common_db_source import CommonDbSourceService
+
+        source = MagicMock(spec=CommonDbSourceService)
+        source.get_tables_name_and_type = CommonDbSourceService.get_tables_name_and_type.__get__(source)
+
+        ctx = MagicMock()
+        ctx.database_schema = schema_name
+        ctx.database_service = "my_service"
+        ctx.database = "my_db"
+        source.context.get.return_value = ctx
+
+        source.source_config.includeTables = True
+        source.source_config.includeViews = False
+        source.source_config.useFqnForFiltering = False
+
+        source.schemas_with_table_listing_errors = set()
+        return source, schema_name, schema_fqn
+
+    def test_listing_error_adds_schema_to_error_set(self):
+        """When query_table_names_and_types raises, the schema FQN is added to the error set."""
+        from metadata.ingestion.source.database.common_db_source import CommonDbSourceService
+
+        source = MagicMock(spec=CommonDbSourceService)
+        source.get_tables_name_and_type = CommonDbSourceService.get_tables_name_and_type.__get__(source)
+
+        ctx = MagicMock()
+        ctx.database_schema = "broken_schema"
+        ctx.database_service = "my_service"
+        ctx.database = "my_db"
+        source.context.get.return_value = ctx
+
+        source.source_config.includeTables = True
+        source.source_config.includeViews = False
+        source.source_config.useFqnForFiltering = False
+        source.schemas_with_table_listing_errors = set()
+
+        source.query_table_names_and_types.side_effect = Exception("connection refused")
+
+        expected_fqn = "my_service.my_db.broken_schema"
+        with patch(
+            "metadata.ingestion.source.database.common_db_source.fqn.build",
+            return_value=expected_fqn,
+        ):
+            list(source.get_tables_name_and_type())
+
+        assert expected_fqn in source.schemas_with_table_listing_errors
+
+    def test_listing_success_leaves_error_set_empty(self):
+        """Successful listing must not add anything to schemas_with_table_listing_errors."""
+        from metadata.ingestion.source.database.common_db_source import CommonDbSourceService
+        from metadata.generated.schema.entity.data.table import TableType
+        from metadata.ingestion.models.topology import TableNameAndType
+
+        source = MagicMock(spec=CommonDbSourceService)
+        source.get_tables_name_and_type = CommonDbSourceService.get_tables_name_and_type.__get__(source)
+
+        ctx = MagicMock()
+        ctx.database_schema = "good_schema"
+        ctx.database_service = "my_service"
+        ctx.database = "my_db"
+        source.context.get.return_value = ctx
+
+        source.source_config.includeTables = True
+        source.source_config.includeViews = False
+        source.source_config.useFqnForFiltering = False
+        source.source_config.tableFilterPattern = None
+        source.schemas_with_table_listing_errors = set()
+
+        source.query_table_names_and_types.return_value = [
+            TableNameAndType(name="orders", type_=TableType.Regular)
+        ]
+        source.standardize_table_name.side_effect = lambda schema, name: name
+        source.get_tag_labels.return_value = None
+
+        with patch(
+            "metadata.ingestion.source.database.common_db_source.filter_by_table",
+            return_value=False,
+        ):
+            list(source.get_tables_name_and_type())
+
+        assert source.schemas_with_table_listing_errors == set()
+
+    def test_listing_error_with_no_fqn_does_not_add_none(self):
+        """If fqn.build returns None (schema not found), nothing should be added to the error set."""
+        from metadata.ingestion.source.database.common_db_source import CommonDbSourceService
+
+        source = MagicMock(spec=CommonDbSourceService)
+        source.get_tables_name_and_type = CommonDbSourceService.get_tables_name_and_type.__get__(source)
+
+        ctx = MagicMock()
+        ctx.database_schema = "missing_schema"
+        ctx.database_service = "my_service"
+        ctx.database = "my_db"
+        source.context.get.return_value = ctx
+
+        source.source_config.includeTables = True
+        source.source_config.includeViews = False
+        source.source_config.useFqnForFiltering = False
+        source.schemas_with_table_listing_errors = set()
+
+        source.query_table_names_and_types.side_effect = Exception("timeout")
+
+        with patch(
+            "metadata.ingestion.source.database.common_db_source.fqn.build",
+            return_value=None,
+        ):
+            list(source.get_tables_name_and_type())
+
+        assert None not in source.schemas_with_table_listing_errors
+        assert len(source.schemas_with_table_listing_errors) == 0