fix: search without prior cognify (#1570)

I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin

## Description

#1548 did not handle multi-tenant case, where graph db context is set
further downstream.

This version adds empty graph logging/handling that works for
multi-tenant case

cognee/api/v1/datasets/datasets.py

@@ -1,4 +1,5 @@
 from uuid import UUID
+from cognee.modules.data.methods import has_dataset_data
 from cognee.modules.users.methods import get_default_user
 from cognee.modules.ingestion import discover_directory_datasets
 from cognee.modules.pipelines.operations.get_pipeline_status import get_pipeline_status
@@ -26,6 +27,16 @@ class datasets:
 
         return await get_dataset_data(dataset.id)
 
+    @staticmethod
+    async def has_data(dataset_id: str) -> bool:
+        from cognee.modules.data.methods import get_dataset
+
+        user = await get_default_user()
+
+        dataset = await get_dataset(user.id, dataset_id)
+
+        return await has_dataset_data(dataset.id)
+
     @staticmethod
     async def get_status(dataset_ids: list[UUID]) -> dict:
         return await get_pipeline_status(dataset_ids, pipeline_name="cognify_pipeline")

cognee/api/v1/search/search.py

@@ -1,6 +1,7 @@
 from uuid import UUID
 from typing import Union, Optional, List, Type
 
+from cognee.infrastructure.databases.graph import get_graph_engine
 from cognee.modules.engine.models.node_set import NodeSet
 from cognee.modules.users.models import User
 from cognee.modules.search.types import SearchResult, SearchType, CombinedSearchResult

cognee/infrastructure/databases/graph/graph_db_interface.py

@@ -159,6 +159,11 @@ class GraphDBInterface(ABC):
     - get_connections
     """
 
+    @abstractmethod
+    async def is_empty(self) -> bool:
+        logger.warning("is_empty() is not implemented")
+        return True
+
     @abstractmethod
     async def query(self, query: str, params: dict) -> List[Any]:
         """

cognee/infrastructure/databases/graph/kuzu/adapter.py

@@ -198,6 +198,15 @@ class KuzuAdapter(GraphDBInterface):
         except FileNotFoundError:
             logger.warning(f"Kuzu S3 storage file not found: {self.db_path}")
 
+    async def is_empty(self) -> bool:
+        query = """
+        MATCH (n)
+        RETURN true
+        LIMIT 1;
+        """
+        query_result = await self.query(query)
+        return len(query_result) == 0
+
     async def query(self, query: str, params: Optional[dict] = None) -> List[Tuple]:
         """
         Execute a Kuzu query asynchronously with automatic reconnection.

cognee/infrastructure/databases/graph/neo4j_driver/adapter.py

@@ -87,6 +87,15 @@ class Neo4jAdapter(GraphDBInterface):
         async with self.driver.session(database=self.graph_database_name) as session:
             yield session
 
+    async def is_empty(self) -> bool:
+        query = """
+        RETURN EXISTS {
+        MATCH (n)
+        } AS node_exists;
+        """
+        query_result = await self.query(query)
+        return not query_result[0]["node_exists"]
+
     @deadlock_retry()
     async def query(
         self,

cognee/modules/data/methods/__init__.py

@@ -23,3 +23,6 @@ from .create_authorized_dataset import create_authorized_dataset
 
 # Check
 from .check_dataset_name import check_dataset_name
+
+# Boolean check
+from .has_dataset_data import has_dataset_data

cognee/modules/data/methods/has_dataset_data.py

@@ -0,0 +1,21 @@
+from uuid import UUID
+
+from sqlalchemy import select
+from sqlalchemy.sql import func
+
+from cognee.infrastructure.databases.relational import get_relational_engine
+from cognee.modules.data.models import DatasetData
+
+
+async def has_dataset_data(dataset_id: UUID) -> bool:
+    db_engine = get_relational_engine()
+
+    async with db_engine.get_async_session() as session:
+        count_query = (
+            select(func.count())
+            .select_from(DatasetData)
+            .where(DatasetData.dataset_id == dataset_id)
+        )
+        count = await session.execute(count_query)
+
+        return count.scalar_one() > 0

cognee/modules/retrieval/cypher_search_retriever.py

@@ -44,6 +44,12 @@ class CypherSearchRetriever(BaseRetriever):
         """
         try:
             graph_engine = await get_graph_engine()
+            is_empty = await graph_engine.is_empty()
+
+            if is_empty:
+                logger.warning("Search attempt on an empty knowledge graph")
+                return []
+
             result = await graph_engine.query(query)
         except Exception as e:
             logger.error("Failed to execture cypher search retrieval: %s", str(e))

cognee/modules/retrieval/graph_completion_retriever.py

@@ -124,6 +124,13 @@ class GraphCompletionRetriever(BaseGraphRetriever):
             - str: A string representing the resolved context from the retrieved triplets, or an
               empty string if no triplets are found.
         """
+        graph_engine = await get_graph_engine()
+        is_empty = await graph_engine.is_empty()
+
+        if is_empty:
+            logger.warning("Search attempt on an empty knowledge graph")
+            return []
+
         triplets = await self.get_triplets(query)
 
         if len(triplets) == 0:

cognee/modules/retrieval/natural_language_retriever.py

@@ -122,6 +122,11 @@ class NaturalLanguageRetriever(BaseRetriever):
               query.
         """
         graph_engine = await get_graph_engine()
+        is_empty = await graph_engine.is_empty()
+
+        if is_empty:
+            logger.warning("Search attempt on an empty knowledge graph")
+            return []
 
         return await self._execute_cypher_query(query, graph_engine)
 

cognee/modules/search/methods/no_access_control_search.py

@@ -1,12 +1,16 @@
 from typing import Any, List, Optional, Tuple, Type, Union
 
+from cognee.infrastructure.databases.graph import get_graph_engine
 from cognee.modules.data.models.Dataset import Dataset
 from cognee.modules.engine.models.node_set import NodeSet
 from cognee.modules.graph.cognee_graph.CogneeGraphElements import Edge
 from cognee.modules.search.types import SearchType
+from cognee.shared.logging_utils import get_logger
 
 from .get_search_type_tools import get_search_type_tools
 
+logger = get_logger()
+
 
 async def no_access_control_search(
     query_type: SearchType,
@@ -32,6 +36,12 @@ async def no_access_control_search(
         save_interaction=save_interaction,
         last_k=last_k,
     )
+    graph_engine = await get_graph_engine()
+    is_empty = await graph_engine.is_empty()
+
+    if is_empty:
+        # TODO: we can log here, but not all search types use graph. Still keeping this here for reviewer input
+        logger.warning("Search attempt on an empty knowledge graph")
     if len(search_tools) == 2:
         [get_completion, get_context] = search_tools
 

cognee/modules/search/methods/search.py

@@ -5,6 +5,8 @@ from uuid import UUID
 from fastapi.encoders import jsonable_encoder
 from typing import Any, List, Optional, Tuple, Type, Union
 
+from cognee.infrastructure.databases.graph import get_graph_engine
+from cognee.shared.logging_utils import get_logger
 from cognee.shared.utils import send_telemetry
 from cognee.context_global_variables import set_database_global_context_variables
 
@@ -27,6 +29,8 @@ from .get_search_type_tools import get_search_type_tools
 from .no_access_control_search import no_access_control_search
 from ..utils.prepare_search_result import prepare_search_result
 
+logger = get_logger()
+
 
 async def search(
     query_text: str,
@@ -329,6 +333,25 @@ async def search_in_datasets_context(
         # Set database configuration in async context for each dataset user has access for
         await set_database_global_context_variables(dataset.id, dataset.owner_id)
 
+        graph_engine = await get_graph_engine()
+        is_empty = await graph_engine.is_empty()
+
+        if is_empty:
+            # TODO: we can log here, but not all search types use graph. Still keeping this here for reviewer input
+            from cognee.modules.data.methods import get_dataset_data
+
+            dataset_data = await get_dataset_data(dataset.id)
+
+            if len(dataset_data) > 0:
+                logger.warning(
+                    f"Dataset '{dataset.name}' has {len(dataset_data)} data item(s) but the knowledge graph is empty. "
+                    "Please run cognify to process the data before searching."
+                )
+            else:
+                logger.warning(
+                    "Search attempt on an empty knowledge graph - no data has been added to this dataset"
+                )
+
         specific_search_tools = await get_search_type_tools(
             query_type=query_type,
             query_text=query_text,

cognee/tests/test_kuzu.py

@@ -47,10 +47,26 @@ async def main():
             pathlib.Path(__file__).parent, "test_data/Quantum_computers.txt"
         )
 
+        from cognee.infrastructure.databases.graph import get_graph_engine
+
+        graph_engine = await get_graph_engine()
+
+        is_empty = await graph_engine.is_empty()
+
+        assert is_empty, "Kuzu graph database is not empty"
+
         await cognee.add([explanation_file_path_quantum], dataset_name)
 
+        is_empty = await graph_engine.is_empty()
+
+        assert is_empty, "Kuzu graph database should be empty before cognify"
+
         await cognee.cognify([dataset_name])
 
+        is_empty = await graph_engine.is_empty()
+
+        assert not is_empty, "Kuzu graph database should not be empty"
+
         from cognee.infrastructure.databases.vector import get_vector_engine
 
         vector_engine = get_vector_engine()
@@ -114,11 +130,10 @@ async def main():
         assert not os.path.isdir(data_root_directory), "Local data files are not deleted"
 
         await cognee.prune.prune_system(metadata=True)
-        from cognee.infrastructure.databases.graph import get_graph_engine
 
-        graph_engine = await get_graph_engine()
+        is_empty = await graph_engine.is_empty()
-        nodes, edges = await graph_engine.get_graph_data()
+
-        assert len(nodes) == 0 and len(edges) == 0, "Kuzu graph database is not empty"
+        assert is_empty, "Kuzu graph database is not empty"
 
     finally:
         # Ensure cleanup even if tests fail

cognee/tests/test_neo4j.py

@@ -35,6 +35,14 @@ async def main():
     explanation_file_path_nlp = os.path.join(
         pathlib.Path(__file__).parent, "test_data/Natural_language_processing.txt"
     )
+    from cognee.infrastructure.databases.graph import get_graph_engine
+
+    graph_engine = await get_graph_engine()
+
+    is_empty = await graph_engine.is_empty()
+
+    assert is_empty, "Graph has to be empty"
+
     await cognee.add([explanation_file_path_nlp], dataset_name)
 
     explanation_file_path_quantum = os.path.join(
@@ -42,9 +50,16 @@ async def main():
     )
 
     await cognee.add([explanation_file_path_quantum], dataset_name)
+    is_empty = await graph_engine.is_empty()
+
+    assert is_empty, "Graph has to be empty before cognify"
 
     await cognee.cognify([dataset_name])
 
+    is_empty = await graph_engine.is_empty()
+
+    assert not is_empty, "Graph shouldn't be empty"
+
     from cognee.infrastructure.databases.vector import get_vector_engine
 
     vector_engine = get_vector_engine()
@@ -117,11 +132,8 @@ async def main():
     assert not os.path.isdir(data_root_directory), "Local data files are not deleted"
 
     await cognee.prune.prune_system(metadata=True)
-    from cognee.infrastructure.databases.graph import get_graph_engine
+    is_empty = await graph_engine.is_empty()
-
+    assert is_empty, "Neo4j graph database is not empty"
-    graph_engine = await get_graph_engine()
-    nodes, edges = await graph_engine.get_graph_data()
-    assert len(nodes) == 0 and len(edges) == 0, "Neo4j graph database is not empty"
 
 
 if __name__ == "__main__":