fix: Add reraising of general exception handling in cognee [COG-1062] (#490)

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

## Description
Add re-raising of errors in general exception handling 

## 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


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Bug Fixes & Stability Improvements**
- Enhanced error handling throughout the system, ensuring issues during
operations like server startup, data processing, and graph management
are properly logged and reported.

- **Refactor**
- Standardized logging practices replace basic output statements,
improving traceability and providing better insights for
troubleshooting.

- **New Features**
- Updated search functionality now returns only unique results,
enhancing data consistency and the overall user experience.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: holchan <61059652+holchan@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>

cognee/api/client.py

@@ -188,6 +188,7 @@ def start_api_server(host: str = "0.0.0.0", port: int = 8000):
     except Exception as e:
         logger.exception(f"Failed to start server: {e}")
         # Here you could add any cleanup code or error recovery code.
+        raise e
 
 
 if __name__ == "__main__":

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

@@ -16,7 +16,7 @@ from cognee.infrastructure.engine import DataPoint
 from cognee.modules.storage.utils import JSONEncoder
 import numpy as np
 
-logger = logging.getLogger("NetworkXAdapter")
+logger = logging.getLogger(__name__)
 
 
 class NetworkXAdapter(GraphDBInterface):
@@ -270,8 +270,8 @@ class NetworkXAdapter(GraphDBInterface):
                             if not isinstance(node["id"], UUID):
                                 node["id"] = UUID(node["id"])
                         except Exception as e:
-                            print(e)
-                            pass
+                            logger.error(e)
+                            raise e
 
                         if isinstance(node.get("updated_at"), int):
                             node["updated_at"] = datetime.fromtimestamp(
@@ -299,8 +299,8 @@ class NetworkXAdapter(GraphDBInterface):
                             edge["source_node_id"] = source_id
                             edge["target_node_id"] = target_id
                         except Exception as e:
-                            print(e)
-                            pass
+                            logger.error(e)
+                            raise e
 
                         if isinstance(edge["updated_at"], int):  # Handle timestamp in milliseconds
                             edge["updated_at"] = datetime.fromtimestamp(
@@ -328,8 +328,9 @@ class NetworkXAdapter(GraphDBInterface):
 
                 await self.save_graph_to_file(file_path)
 
-        except Exception:
+        except Exception as e:
             logger.error("Failed to load graph from file: %s", file_path)
+            raise e
 
     async def delete_graph(self, file_path: str = None):
         """Asynchronously delete the graph file from the filesystem."""
@@ -345,6 +346,7 @@ class NetworkXAdapter(GraphDBInterface):
             logger.info("Graph deleted successfully.")
         except Exception as error:
             logger.error("Failed to delete graph: %s", error)
+            raise error
 
     async def get_filtered_graph_data(
         self, attribute_filters: List[Dict[str, List[Union[str, int]]]]

cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py

@@ -303,9 +303,10 @@ class SQLAlchemyAdapter:
                 await connection.execute(text("DROP TABLE IF EXISTS group_permission CASCADE"))
                 await connection.execute(text("DROP TABLE IF EXISTS permissions CASCADE"))
                 # Add more DROP TABLE statements for other tables as needed
-                print("Database tables dropped successfully.")
+                logger.debug("Database tables dropped successfully.")
             except Exception as e:
-                print(f"Error dropping database tables: {e}")
+                logger.error(f"Error dropping database tables: {e}")
+                raise e
 
     async def create_database(self):
         if self.engine.dialect.name == "sqlite":
@@ -340,6 +341,7 @@ class SQLAlchemyAdapter:
                             await connection.execute(drop_table_query)
                         metadata.clear()
         except Exception as e:
-            print(f"Error deleting database: {e}")
+            logger.error(f"Error deleting database: {e}")
+            raise e
 
-        print("Database deleted successfully.")
+        logger.info("Database deleted successfully.")

cognee/modules/chunking/TextChunker.py

@@ -1,10 +1,12 @@
-from typing import Optional
+import logging
 from uuid import NAMESPACE_OID, uuid5
 
 from cognee.tasks.chunks import chunk_by_paragraph
 
 from .models.DocumentChunk import DocumentChunk
 
+logger = logging.getLogger(__name__)
+
 
 class TextChunker:
     document = None
@@ -76,7 +78,8 @@ class TextChunker:
                                 },
                             )
                         except Exception as e:
-                            print(e)
+                            logger.error(e)
+                            raise e
                         paragraph_chunks = [chunk_data]
                         self.chunk_size = chunk_data["word_count"]
                         self.token_count = chunk_data["token_count"]
@@ -97,4 +100,5 @@ class TextChunker:
                     _metadata={"index_fields": ["text"]},
                 )
             except Exception as e:
-                print(e)
+                logger.error(e)
+                raise e

cognee/modules/data/operations/detect_language.py

@@ -34,5 +34,6 @@ async def detect_language(text: str):
 
     except Exception as e:
         logger.error(f"Unexpected error: {e}")
+        raise e
 
     return None

cognee/modules/graph/cognee_graph/CogneeGraph.py

@@ -152,6 +152,7 @@ class CogneeGraph(CogneeAbstractGraph):
 
         except Exception as ex:
             print(f"Error mapping vector distances to edges: {ex}")
+            raise ex
 
     async def calculate_top_triplet_importances(self, k: int) -> List:
         min_heap = []

cognee/modules/retrieval/description_to_codepart_search.py

@@ -11,6 +11,8 @@ from cognee.shared.utils import send_telemetry
 from cognee.modules.search.methods import search
 from cognee.infrastructure.llm.get_llm_client import get_llm_client
 
+logger = logging.getLogger(__name__)
+
 
 async def code_description_to_code_part_search(
     query: str, include_docs=False, user: User = None, top_k=5
@@ -154,8 +156,9 @@ if __name__ == "__main__":
         user = None
         try:
             results = await code_description_to_code_part_search(query, user)
-            print("Retrieved Code Parts:", results)
+            logger.debug("Retrieved Code Parts:", results)
         except Exception as e:
-            print(f"An error occurred: {e}")
+            logger.error(f"An error occurred: {e}")
+            raise e
 
     asyncio.run(main())

cognee/tasks/repo_processor/get_local_dependencies.py

@@ -3,6 +3,7 @@ import asyncio
 import sys
 from contextlib import contextmanager
 from pathlib import Path
+from pickle import UnpicklingError
 from typing import List, Dict, Optional
 
 import aiofiles
@@ -60,9 +61,22 @@ def _update_code_entity(script: jedi.Script, code_entity: Dict[str, any]) -> Non
             code_entity["full_name"] = getattr(result, "full_name", None)
             code_entity["module_name"] = getattr(result, "module_name", None)
             code_entity["module_path"] = getattr(result, "module_path", None)
+    except KeyError as e:
+        # TODO: See if there is a way to handle KeyError properly
+        logger.error(f"Failed to analyze code entity {code_entity['name']}: {e}")
+        return
+    except UnpicklingError as e:
+        # TODO: See if there is a way to handle UnpicklingError properly
+        logger.error(f"Failed to analyze code entity {code_entity['name']}: {e}")
+        return
+    except EOFError as e:
+        # TODO: See if there is a way to handle EOFError properly
+        logger.error(f"Failed to analyze code entity {code_entity['name']}: {e}")
+        return
     except Exception as e:
         # logging.warning(f"Failed to analyze code entity {code_entity['name']}: {e}")
         logger.error(f"Failed to analyze code entity {code_entity['name']}: {e}")
+        raise e
 
 
 async def _extract_dependencies(script_path: str) -> List[str]: