fix: fix tomasonjo (neo4j) issues

Author: YoanSallami

coverage-badge.svg

@@ -2,6 +2,8 @@
 
 import copy
 import re
+from typing import Any
+from typing import Dict
 
 from synalinks.src.utils.naming import to_snake_case
 
@@ -72,7 +74,7 @@ async def update(self, data_model, threshold=0.8):
             f"{self.__class__} should implement the `update()` method"
         )
 
-    async def query(self, query):
+    async def query(self, query: str, params: Dict[str, Any] = None, **kwargs):
         raise NotImplementedError(
             f"{self.__class__} should implement the `query()` method"
         )

synalinks/src/knowledge_bases/database_adapters/database_adapter.py

@@ -31,6 +31,7 @@ def __init__(
             index_name=index_name,
             embedding_model=embedding_model,
         )
+        self.db = os.getenv("NEO4J_DATABASE", "neo4j")
         self.username = os.getenv("NEO4J_USERNAME", "neo4j")
         self.password = os.getenv("NEO4J_PASSWORD", "neo4j")
 
@@ -52,10 +53,14 @@ def __init__(
 
         if wipe_on_start:
             asyncio.get_event_loop().run_until_complete(
-                self.query("MATCH (n)-[r]->() DELETE n, r"),
-            )
-            asyncio.get_event_loop().run_until_complete(
-                self.query("MATCH (m) DELETE m"),
+                self.query(
+                    """
+                    MATCH (n)
+                    CALL (n) {
+                        DETACH DELETE n
+                    } IN TRANSACTIONS OF 10000 ROWS
+                    """
+                )
             )
 
         query = "\n".join(
@@ -101,16 +106,17 @@ def __init__(
                 self.query("CALL db.awaitIndexes(300)"),
             )
 
-    async def query(self, query: str, params: Dict[str, Any] = None):
+    async def query(self, query: str, params: Dict[str, Any] = None, **kwargs):
         driver = neo4j.GraphDatabase.driver(
             self.index_name, auth=(self.username, self.password)
         )
         try:
-            if params:
-                records, _, _ = driver.execute_query(query, **params, database_="neo4j")
-            else:
-                records, _, _ = driver.execute_query(query, database_="neo4j")
-            return records
+            with driver.session(database=self.db) as session:
+                if params:
+                    result = session.run(query, **params, **kwargs)
+                else:
+                    result = session.run(query, **kwargs)
+                return list(result)
         finally:
             driver.close()
 

synalinks/src/knowledge_bases/database_adapters/neo4j_adapter.py

@@ -1,5 +1,8 @@
 # License Apache 2.0: (c) 2025 Yoan Sallami (Synalinks Team)
 
+from typing import Any
+from typing import Dict
+
 from synalinks.src.api_export import synalinks_export
 from synalinks.src.backend import is_symbolic_data_model
 from synalinks.src.backend.config import maybe_initialize_telemetry
@@ -33,8 +36,9 @@ class IsPartOf(synalinks.Relation):
         model="ollama/mxbai-embed-large"
     )
 
-    os.environ["NEO4J_USERNAME"] = "your-neo4j-username"
-    os.environ["NEO4J_PASSWORD"] = "your-neo4j-password"
+    os.environ["NEO4J_DATABASE"] = "your-neo4j-db" # (Default to "neo4j")
+    os.environ["NEO4J_USERNAME"] = "your-neo4j-username" # (Default to "neo4j")
+    os.environ["NEO4J_PASSWORD"] = "your-neo4j-password" # (Default to "neo4j")
 
     knowledge_base = synalinks.KnowledgeBase(
         index_name="neo4j://localhost:7687",
@@ -107,7 +111,7 @@ async def update(
         maybe_initialize_telemetry()
         return await self.adapter.update(data_model)
 
-    async def query(self, query: str):
+    async def query(self, query: str, params: Dict[str, Any] = None, **kwargs):
         """Execute a query against the knowledge base.
 
         Args:
@@ -118,7 +122,7 @@ async def query(self, query: str):
             (GenericResult): the query results
         """
         maybe_initialize_telemetry()
-        return await self.adapter.query(query)
+        return await self.adapter.query(query, params=params, **kwargs)
 
     async def similarity_search(
         self,

synalinks/src/knowledge_bases/knowledge_base.py

@@ -8,7 +8,6 @@
 from synalinks.src.programs.program import Program
 from synalinks.src.utils.tool_utils import Tool
 
-
 _fn_END = "finish"
 
 
@@ -217,7 +216,9 @@ def __init__(
         for fn in self.functions:
             self.labels.append(Tool(fn).name())
 
-        assert _fn_END not in self.labels, f"'{_fn_END}' is a reserved keyword and cannot be used as function name"
+        assert _fn_END not in self.labels, (
+            f"'{_fn_END}' is a reserved keyword and cannot be used as function name"
+        )
 
         self.labels.append(_fn_END)
 

synalinks/src/modules/agents/react_agent.py

@@ -3,7 +3,7 @@
 from synalinks.src.api_export import synalinks_export
 
 # Unique source of truth for the version number.
-__version__ = "0.3.006"
+__version__ = "0.3.007"
 
 
 @synalinks_export("synalinks.version")