index to neo4j working and tested. check queires next.

.gitignore

@@ -5,4 +5,7 @@ book.txt
 lightrag-dev/
 .idea/
 dist/
-env/
+env/
+local_neo4jWorkDir/
+local_neo4jWorkDir.bak/
+neo4jWorkDir/

get_all_edges_nx.py

@@ -0,0 +1,34 @@
+import networkx as nx
+
+G = nx.read_graphml('./dickensTestEmbedcall/graph_chunk_entity_relation.graphml')
+
+def get_all_edges_and_nodes(G):
+    # Get all edges and their properties
+    edges_with_properties = []
+    for u, v, data in G.edges(data=True):
+        edges_with_properties.append({
+            'start': u,
+            'end': v,
+            'label': data.get('label', ''),  # Assuming 'label' is used for edge type
+            'properties': data,
+            'start_node_properties': G.nodes[u],
+            'end_node_properties': G.nodes[v]
+        })
+
+    return edges_with_properties
+
+# Example usage
+if __name__ == "__main__":
+    # Assume G is your NetworkX graph loaded from Neo4j
+
+    all_edges = get_all_edges_and_nodes(G)
+    
+    # Print all edges and node properties
+    for edge in all_edges:
+        print(f"Edge Label: {edge['label']}")
+        print(f"Edge Properties: {edge['properties']}")
+        print(f"Start Node: {edge['start']}")
+        print(f"Start Node Properties: {edge['start_node_properties']}")
+        print(f"End Node: {edge['end']}")
+        print(f"End Node Properties: {edge['end_node_properties']}")
+        print("---")

lightrag/kg/neo4j.py

@@ -4,24 +4,42 @@ import os
 from dataclasses import dataclass
 from typing import Any, Union, cast
 import numpy as np
-from nano_vectordb import NanoVectorDB
 import inspect
+# import package.common.utils as utils
+from lightrag.utils import load_json, logger, write_json
+from ..base import (
+    BaseGraphStorage
+)
+from neo4j import GraphDatabase, exceptions as neo4jExceptions
 
 
+from tenacity import (
+    retry,
+    stop_after_attempt,
+    wait_exponential,
+    retry_if_exception_type,
+)
+
+
+
+
+
+# @TODO: catch and retry "ERROR:neo4j.io:Failed to write data to connection ResolvedIPv4Address"
+#        during indexing.
 
 
-#  import package.common.utils as utils
 
 
-from lightrag.utils import load_json, logger, write_json
-from ..base import (
-    BaseGraphStorage
-)
-from neo4j import GraphDatabase
 # Replace with your actual URI, username, and password
+#local
 URI = "neo4j://localhost:7687"
 USERNAME = "neo4j"
-PASSWORD = "your_password"
+PASSWORD = "password"
+
+#aura
+# URI = "neo4j+s://91fbae6c.databases.neo4j.io"
+# USERNAME = "neo4j"
+# PASSWORD = "KWKPXfXcClDbUlmDdGgIQhU5mL1N4E_2CJp2BDFbEbw"
 # Create a driver object
 
 
@@ -33,7 +51,7 @@ class GraphStorage(BaseGraphStorage):
 
     def __post_init__(self):
         # self._graph = preloaded_graph or nx.Graph()
-        self._driver = GraphDatabase.driver("neo4j+s://91fbae6c.databases.neo4j.io", auth=("neo4j", "KWKPXfXcClDbUlmDdGgIQhU5mL1N4E_2CJp2BDFbEbw"))
+        self._driver = GraphDatabase.driver(URI, auth=(USERNAME, PASSWORD))
         self._node_embed_algorithms = {
             "node2vec": self._node2vec_embed,
         }
@@ -129,13 +147,11 @@ class GraphStorage(BaseGraphStorage):
 
     # degree = session.read_transaction(get_edge_degree, 1, 2)
     async def edge_degree(self, src_id: str, tgt_id: str) -> int:
-        entity_name__label_source = src_id.strip('\"')
+        entity_name_label_source = src_id.strip('\"')
         entity_name_label_target = tgt_id.strip('\"')
         with self._driver.session()  as session:
-            query =  """MATCH (n1:`{node_label1}`)-[r]-(n2:`{node_label2}`)
-                RETURN count(r) AS degree""".format(entity_name__label_source=entity_name__label_source, 
-                                                    entity_name_label_target=entity_name_label_target)
-
+            query =  f"""MATCH (n1:`{entity_name_label_source}`)-[r]-(n2:`{entity_name_label_target}`)
+                RETURN count(r) AS degree"""
             result = session.run(query)        
             record = result.single()
             logger.info(
@@ -144,7 +160,7 @@ class GraphStorage(BaseGraphStorage):
             return record["degree"]
     
     async def get_edge(self, source_node_id: str, target_node_id: str) -> Union[dict, None]:
-        entity_name__label_source = source_node_id.strip('\"')
+        entity_name_label_source = source_node_id.strip('\"')
         entity_name_label_target = target_node_id.strip('\"')
         """
         Find all edges between nodes of two given labels
@@ -156,28 +172,25 @@ class GraphStorage(BaseGraphStorage):
         Returns:
             list: List of all relationships/edges found
         """
-        with self._driver.session() as session:
+        with self._driver.session()  as session:
             query = f"""
-            MATCH (source:`{entity_name__label_source}`)-[r]-(target:`{entity_name_label_target}`)
-            RETURN r
-            """
+            MATCH (start:`{entity_name_label_source}`)-[r]->(end:`{entity_name_label_target}`)
+            RETURN properties(r) as edge_properties
+            LIMIT 1
+            """.format(entity_name_label_source=entity_name_label_source, entity_name_label_target=entity_name_label_target)
             
-            result = session.run(query)
-            for logrecord in result:
+            result = session.run(query)           
+            record = result.single()
+            if record:
+                result = dict(record["edge_properties"])
                 logger.info(
-                    f'{inspect.currentframe().f_code.co_name}:query:{query}:result:{logrecord["r"]}'
-                )   
-
-
-            return [record["r"] for record in result]
+                    f'{inspect.currentframe().f_code.co_name}:query:{query}:result:{result}'
+                )     
+                return result
+            else:
+                return None
         
 
-
-    async def get_node_edges(self, source_node_id: str):
-        if self._graph.has_node(source_node_id):
-            return list(self._graph.edges(source_node_id))
-        return None
-
     async def get_node_edges(self, source_node_id: str):
         node_label = source_node_id.strip('\"')
           
@@ -208,8 +221,8 @@ class GraphStorage(BaseGraphStorage):
                 target_label = list(connected_node.labels)[0] if connected_node and connected_node.labels else None
                 
                 if source_label and target_label:
-                    print (f"appending: {[source_label, target_label]}")
-                    edges.append([source_label, target_label])
+                    print (f"appending: {(source_label, target_label)}")
+                    edges.append((source_label, target_label))
             
             return edges
 
@@ -218,57 +231,54 @@ class GraphStorage(BaseGraphStorage):
             return edges
 
 
-        # try:
-        #     with self._driver.session() as session:
-        #         if self.has_node(node_label):
-        #             edges = session.read_transaction(fetch_edges,node_label)
-        #             return list(edges)
-        #     return edges
-        # finally:
-        #     print ("consider closign driver here")
-        #     # driver.close()
     
-    from typing import List, Tuple
-    async def get_node_connections(driver: GraphDatabase.driver, label: str) -> List[Tuple[str, str]]:
-        def run_query(tx):
-            query = f"""
-            MATCH (n:`{label}`)
-            OPTIONAL MATCH (n)-[r]-(connected)
-            RETURN n, r, connected
-            """
-            results = tx.run(query)
+    # from typing import List, Tuple
+    # async def get_node_connections(driver: GraphDatabase.driver, label: str) -> List[Tuple[str, str]]:
+    #     def get_connections_for_node(tx):
+    #         query = f"""
+    #         MATCH (n:`{label}`)
+    #         OPTIONAL MATCH (n)-[r]-(connected)
+    #         RETURN n, r, connected
+    #         """
+    #         results = tx.run(query)
             
-            connections = []
-            for record in results:
-                source_node = record['n']
-                connected_node = record['connected']
+            
+    #         connections = []
+    #         for record in results:
+    #             source_node = record['n']
+    #             connected_node = record['connected']
                 
-                source_label = list(source_node.labels)[0] if source_node.labels else None
-                target_label = list(connected_node.labels)[0] if connected_node and connected_node.labels else None
+    #             source_label = list(source_node.labels)[0] if source_node.labels else None
+    #             target_label = list(connected_node.labels)[0] if connected_node and connected_node.labels else None
                 
-                if source_label and target_label:
-                    connections.append((source_label, target_label))
-            
-            return connections
+    #             if source_label and target_label:
+    #                 connections.append((source_label, target_label))
+
+    #         logger.info(
+    #             f'{inspect.currentframe().f_code.co_name}:query:{query}:result:{connections}'
+    #         ) 
+    #         return connections
 
-        with driver.session() as session:
-            return session.read_transaction(run_query)
+    #     with driver.session() as session:
+              
+    #         return session.read_transaction(get_connections_for_node)
 
         
 
 
 
     #upsert_node
+
+    @retry(
+        stop=stop_after_attempt(3),
+        wait=wait_exponential(multiplier=1, min=4, max=10),
+        retry=retry_if_exception_type((neo4jExceptions.ServiceUnavailable, neo4jExceptions.TransientError, neo4jExceptions.WriteServiceUnavailable)),
+    )
     async def upsert_node(self, node_id: str, node_data: dict[str, str]):
         label = node_id.strip('\"')
         properties = node_data
         """
         Upsert a node with the given label and properties within a transaction.
-        If a node with the same label exists, it will:
-        - Update existing properties with new values
-        - Add new properties that don't exist
-        If no node exists, creates a new node with all properties.
-        
         Args:
             label: The node label to search for and apply
             properties: Dictionary of node properties
@@ -355,7 +365,7 @@ class GraphStorage(BaseGraphStorage):
 
             result = tx.run(query, properties=edge_properties)
             logger.info(
-                f'{inspect.currentframe().f_code.co_name}:query:{query}:result:{None}'
+                f'{inspect.currentframe().f_code.co_name}:query:{query}:edge_properties:{edge_properties}'
             )               
             return result.single()
             
@@ -369,6 +379,8 @@ class GraphStorage(BaseGraphStorage):
             # return result
 
     async def _node2vec_embed(self):
+        print ("this is never called.  checking to be sure.")
+        
         # async def _node2vec_embed(self):
         with self._driver.session()  as session:
             #Define the Cypher query

lightrag/lightrag.py

@@ -102,8 +102,8 @@ class LightRAG:
 
     # module = importlib.import_module('kg.neo4j')
     # Neo4JStorage = getattr(module, 'GraphStorage')
-
     if True==True:
+        print ("using KG")
         graph_storage_cls: Type[BaseGraphStorage] = Neo4JStorage
     else:
         graph_storage_cls: Type[BaseGraphStorage] = NetworkXStorage

lightrag/storage.py

@@ -235,7 +235,7 @@ class NetworkXStorage(BaseGraphStorage):
 
     async def _node2vec_embed(self):
         from graspologic import embed
-
+        print ("is this ever called?")
         embeddings, nodes = embed.node2vec_embed(
             self._graph,
             **self.global_config["node2vec_params"],

test.py

@@ -1,15 +1,34 @@
 import os
 from lightrag import LightRAG, QueryParam
 from lightrag.llm import gpt_4o_mini_complete, gpt_4o_complete
-
+from pprint import pprint
 #########
 # Uncomment the below two lines if running in a jupyter notebook to handle the async nature of rag.insert()
 # import nest_asyncio 
 # nest_asyncio.apply() 
 #########
 
-WORKING_DIR = "./dickens"
+WORKING_DIR = "./dickensTestEmbedcall"
+
+
+# G = nx.read_graphml('./dickensTestEmbedcall/graph_chunk_entity_relation.graphml')
+# nx.write_gexf(G, "graph_chunk_entity_relation.gefx")
+
+import networkx as nx
+from networkx_query import search_nodes, search_edges
+G = nx.read_graphml('./dickensTestEmbedcall/graph_chunk_entity_relation.graphml')
+query = {}  # Empty query matches all nodes
+result = search_nodes(G, query)
+
+# Extract node IDs from the result
+node_ids = sorted([node for node in result])
+
+print("All node IDs in the graph:")
+pprint(node_ids)
+raise Exception
+
 
+# raise Exception
 
 if not os.path.exists(WORKING_DIR):
     os.mkdir(WORKING_DIR)

testkg.py

@@ -8,8 +8,7 @@ from lightrag.llm import gpt_4o_mini_complete, gpt_4o_complete
 # nest_asyncio.apply() 
 #########
 
-WORKING_DIR = "./neo4jWorkDir"
-
+WORKING_DIR = "./local_neo4jWorkDir"
 
 if not os.path.exists(WORKING_DIR):
     os.mkdir(WORKING_DIR)