Merge branch 'dev' into feature/cog-3187-feedback-enrichment

README.md

@@ -71,7 +71,7 @@ Build dynamic memory for Agents and replace RAG using scalable, modular ECL (Ext
 
 ## Get Started
 
-Get started quickly with a Google Colab  <a href="https://colab.research.google.com/drive/1jHbWVypDgCLwjE71GSXhRL3YxYhCZzG1?usp=sharing">notebook</a> , <a href="https://deepnote.com/workspace/cognee-382213d0-0444-4c89-8265-13770e333c02/project/cognee-demo-78ffacb9-5832-4611-bb1a-560386068b30/notebook/Notebook-1-75b24cda566d4c24ab348f7150792601?utm_source=share-modal&utm_medium=product-shared-content&utm_campaign=notebook&utm_content=78ffacb9-5832-4611-bb1a-560386068b30">Deepnote notebook</a> or  <a href="https://github.com/topoteretes/cognee/tree/main/cognee-starter-kit">starter repo</a>
+Get started quickly with a Google Colab  <a href="https://colab.research.google.com/drive/12Vi9zID-M3fpKpKiaqDBvkk98ElkRPWy?usp=sharing">notebook</a> , <a href="https://deepnote.com/workspace/cognee-382213d0-0444-4c89-8265-13770e333c02/project/cognee-demo-78ffacb9-5832-4611-bb1a-560386068b30/notebook/Notebook-1-75b24cda566d4c24ab348f7150792601?utm_source=share-modal&utm_medium=product-shared-content&utm_campaign=notebook&utm_content=78ffacb9-5832-4611-bb1a-560386068b30">Deepnote notebook</a> or  <a href="https://github.com/topoteretes/cognee/tree/main/cognee-starter-kit">starter repo</a>
 
 
 ## About cognee
@@ -224,12 +224,12 @@ We now have a paper you can cite:
 
 ```bibtex
 @misc{markovic2025optimizinginterfaceknowledgegraphs,
-      title={Optimizing the Interface Between Knowledge Graphs and LLMs for Complex Reasoning}, 
+      title={Optimizing the Interface Between Knowledge Graphs and LLMs for Complex Reasoning},
       author={Vasilije Markovic and Lazar Obradovic and Laszlo Hajdu and Jovan Pavlovic},
       year={2025},
       eprint={2505.24478},
       archivePrefix={arXiv},
       primaryClass={cs.AI},
-      url={https://arxiv.org/abs/2505.24478}, 
+      url={https://arxiv.org/abs/2505.24478},
 }
 ```

cognee/api/v1/search/search.py

@@ -1,7 +1,6 @@
 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
@@ -9,9 +8,6 @@ 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(

cognee/infrastructure/databases/graph/graph_db_interface.py

@@ -159,11 +159,6 @@ 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

@@ -198,15 +198,6 @@ 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

@@ -87,15 +87,6 @@ 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,
@@ -1076,7 +1067,7 @@ class Neo4jAdapter(GraphDBInterface):
         query_nodes = f"""
         MATCH (n)
         WHERE {where_clause}
-        RETURN ID(n) AS id, labels(n) AS labels, properties(n) AS properties
+        RETURN n.id AS id, labels(n) AS labels, properties(n) AS properties
         """
         result_nodes = await self.query(query_nodes)
 
@@ -1091,7 +1082,7 @@ class Neo4jAdapter(GraphDBInterface):
         query_edges = f"""
         MATCH (n)-[r]->(m)
         WHERE {where_clause} AND {where_clause.replace("n.", "m.")}
-        RETURN ID(n) AS source, ID(m) AS target, TYPE(r) AS type, properties(r) AS properties
+        RETURN n.id AS source, n.id AS target, TYPE(r) AS type, properties(r) AS properties
         """
         result_edges = await self.query(query_edges)
 

cognee/infrastructure/files/utils/guess_file_type.py

@@ -124,6 +124,12 @@ def guess_file_type(file: BinaryIO) -> filetype.Type:
     """
     file_type = filetype.guess(file)
 
+    # If file type could not be determined consider it a plain text file as they don't have magic number encoding
+    if file_type is None:
+        from filetype.types.base import Type
+
+        file_type = Type("text/plain", "txt")
+
     if file_type is None:
         raise FileTypeException(f"Unknown file detected: {file.name}.")
 

cognee/modules/pipelines/operations/run_tasks_distributed.py

@@ -88,6 +88,7 @@ async def run_tasks_distributed(
     pipeline_name: str = "unknown_pipeline",
     context: dict = None,
     incremental_loading: bool = False,
+    data_per_batch: int = 20,
 ):
     if not user:
         user = await get_default_user()

cognee/tests/test_kuzu.py

@@ -47,26 +47,10 @@ 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()
@@ -130,10 +114,11 @@ 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()
+        graph_engine = await get_graph_engine()
-
+        nodes, edges = await graph_engine.get_graph_data()
-        assert is_empty, "Kuzu graph database is not empty"
+        assert len(nodes) == 0 and len(edges) == 0, "Kuzu graph database is not empty"
 
     finally:
         # Ensure cleanup even if tests fail

cognee/tests/test_neo4j.py

@@ -35,14 +35,6 @@ 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(
@@ -50,16 +42,9 @@ 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()
@@ -132,8 +117,11 @@ async def main():
     assert not os.path.isdir(data_root_directory), "Local data files are not deleted"
 
     await cognee.prune.prune_system(metadata=True)
-    is_empty = await graph_engine.is_empty()
+    from cognee.infrastructure.databases.graph import get_graph_engine
-    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

@@ -1,21 +0,0 @@
-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 != []