Merge remote-tracking branch 'origin/dev' into feature/cog-3014-refactor-delete-feature

cognee/api/v1/add/add.py

@@ -41,6 +41,7 @@ async def add(
     extraction_rules: Optional[Dict[str, Any]] = None,
     tavily_config: Optional[BaseModel] = None,
     soup_crawler_config: Optional[BaseModel] = None,
+    data_per_batch: Optional[int] = 20,
 ):
     """
     Add data to Cognee for knowledge graph processing.
@@ -235,6 +236,7 @@ async def add(
         vector_db_config=vector_db_config,
         graph_db_config=graph_db_config,
         incremental_loading=incremental_loading,
+        data_per_batch=data_per_batch,
     ):
         pipeline_run_info = run_info
 

cognee/api/v1/cognify/cognify.py

@@ -51,6 +51,7 @@ async def cognify(
     incremental_loading: bool = True,
     custom_prompt: Optional[str] = None,
     temporal_cognify: bool = False,
+    data_per_batch: int = 20,
 ):
     """
     Transform ingested data into a structured knowledge graph.
@@ -228,6 +229,7 @@ async def cognify(
         graph_db_config=graph_db_config,
         incremental_loading=incremental_loading,
         pipeline_name="cognify_pipeline",
+        data_per_batch=data_per_batch,
     )
 
 

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
@@ -8,6 +9,9 @@ from cognee.modules.users.methods import get_default_user
 from cognee.modules.search.methods import search as search_function
 from cognee.modules.data.methods import get_authorized_existing_datasets
 from cognee.modules.data.exceptions import DatasetNotFoundError
+from cognee.shared.logging_utils import get_logger
+
+logger = get_logger()
 
 
 async def search(
@@ -175,6 +179,13 @@ async def search(
         if not datasets:
             raise DatasetNotFoundError(message="No datasets 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 []
+
     filtered_search_results = await search_function(
         query_text=query_text,
         query_type=query_type,

cognee/infrastructure/databases/graph/graph_db_interface.py

@@ -39,6 +39,11 @@ 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

@@ -197,6 +197,15 @@ 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

@@ -86,6 +86,15 @@ 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/pipelines/operations/pipeline.py

@@ -36,6 +36,7 @@ async def run_pipeline(
     graph_db_config: Optional[dict] = None,
     incremental_loading: bool = False,
     context: Optional[Dict] = None,
+    data_per_batch: int = 20,
 ):
     validate_pipeline_tasks(tasks)
     await setup_and_check_environment(vector_db_config, graph_db_config)
@@ -51,6 +52,7 @@ async def run_pipeline(
             pipeline_name=pipeline_name,
             incremental_loading=incremental_loading,
             context=context,
+            data_per_batch=data_per_batch,
         ):
             yield run_info
 
@@ -63,6 +65,7 @@ async def run_pipeline_per_dataset(
     pipeline_name: str = "custom_pipeline",
     incremental_loading=False,
     context: Optional[Dict] = None,
+    data_per_batch: int = 20,
 ):
     # Will only be used if ENABLE_BACKEND_ACCESS_CONTROL is set to True
     await set_database_global_context_variables(dataset.id, dataset.owner_id)
@@ -78,7 +81,7 @@ async def run_pipeline_per_dataset(
         return
 
     pipeline_run = run_tasks(
-        tasks, dataset, data, user, pipeline_name, context, incremental_loading
+        tasks, dataset, data, user, pipeline_name, context, incremental_loading, data_per_batch
     )
 
     async for pipeline_run_info in pipeline_run:

cognee/modules/pipelines/operations/run_tasks.py

@@ -59,6 +59,7 @@ async def run_tasks(
     pipeline_name: str = "unknown_pipeline",
     context: Optional[Dict] = None,
     incremental_loading: bool = False,
+    data_per_batch: int = 20,
 ):
     if not user:
         user = await get_default_user()
@@ -81,29 +82,34 @@ async def run_tasks(
         if incremental_loading:
             data = await resolve_data_directories(data)
 
-        # Create async tasks per data item that will run the pipeline for the data item
+        # Create and gather batches of async tasks of data items that will run the pipeline for the data item
-        data_item_tasks = [
+        results = []
-            asyncio.create_task(
+        for start in range(0, len(data), data_per_batch):
-                run_tasks_data_item(
+            data_batch = data[start : start + data_per_batch]
-                    data_item,
+
-                    dataset,
+            data_item_tasks = [
-                    tasks,
+                asyncio.create_task(
-                    pipeline_name,
+                    run_tasks_data_item(
-                    pipeline_id,
+                        data_item,
-                    pipeline_run_id,
+                        dataset,
-                    {
+                        tasks,
-                        **(context or {}),
+                        pipeline_name,
-                        "user": user,
+                        pipeline_id,
-                        "data": data_item,
+                        pipeline_run_id,
-                        "dataset": dataset,
+                        {
-                    },
+                            **(context or {}),
-                    user,
+                            "user": user,
-                    incremental_loading,
+                            "data": data_item,
+                            "dataset": dataset,
+                        },
+                        user,
+                        incremental_loading,
+                    )
                 )
-            )
+                for data_item in data_batch
-            for data_item in data
+            ]
-        ]
+
-        results = await asyncio.gather(*data_item_tasks)
+            results.extend(await asyncio.gather(*data_item_tasks))
 
         # Remove skipped data items from results
         results = [result for result in results if result]

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__":

cognee/tests/unit/api/test_search.py

@@ -0,0 +1,21 @@
+import pytest
+import cognee
+
+
+@pytest.mark.asyncio
+async def test_empty_search_raises_SearchOnEmptyGraphError_on_empty_graph():
+    await cognee.prune.prune_data()
+    await cognee.prune.prune_system(metadata=True)
+    await cognee.add("Sample input")
+    result = await cognee.search("Sample query")
+    assert result == []
+
+
+@pytest.mark.asyncio
+async def test_empty_search_doesnt_raise_SearchOnEmptyGraphError():
+    await cognee.prune.prune_data()
+    await cognee.prune.prune_system(metadata=True)
+    await cognee.add("Sample input")
+    await cognee.cognify()
+    result = await cognee.search("Sample query")
+    assert result != []