fix: search without prior cognify (#1548)

<!-- .github/pull_request_template.md -->

## Description
<!--
Please provide a clear, human-generated description of the changes in
this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->

Running search when `cognee.add()` is called, but `cognee.cognify()`
wasn't called yet goes through the whole search operation to throw a
cryptic error:
```
Error during graph projection: EntityNotFoundError: Empty graph projected from the database. (Status code: 404)
```

## How to reproduce
modify `dynamic_steps_example.py` to not run cognify

## This PR

Checks graph before searching, and throws an informative exception to
ensure cognify was run

| Logs Before | Logs After |
|--------------|------------|
| `Error during graph projection: EntityNotFoundError: Empty graph
projected from the database. (Status code: 404)` |
`2025-10-17T11:05:58.465315 [warning ] Search attempt on an empty
knowledge graph [cognee.shared.logging_utils]` |

## Type of Change
<!-- Please check the relevant option -->
- [x] Bug fix (non-breaking change that fixes an issue)
- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):

## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->

## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **I have tested my changes thoroughly before submitting this PR**
- [ ] **This PR contains minimal changes necessary to address the
issue/feature**
- [ ] My code follows the project's coding standards and style
guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
- [ ] I have linked any relevant issues in the description
- [ ] My commits have clear and descriptive messages

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

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

@@ -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/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()
-        nodes, edges = await graph_engine.get_graph_data()
-        assert len(nodes) == 0 and len(edges) == 0, "Kuzu graph database is not empty"
+        is_empty = await graph_engine.is_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
-
-    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"
+    is_empty = await graph_engine.is_empty()
+    assert is_empty, "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 != []