From fba2356c8150ab6b5d543da1d12d66e9d5299e9f Mon Sep 17 00:00:00 2001
From: yangdx <gzdaniel@me.com>
Date: Fri, 26 Sep 2025 10:02:01 +0800
Subject: [PATCH] Move user_prompt to system prompt

- Refactor query prompt handling to separate user prompts in system context
- Simplify user_query to only contain query
- Apply changes to both kg_query and naive_query
---
 lightrag/operate.py | 20 +++++++++-----------
 lightrag/prompt.py  |  8 ++++++++
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/lightrag/operate.py b/lightrag/operate.py
index 685e86a8..dc4ae1df 100644
--- a/lightrag/operate.py
+++ b/lightrag/operate.py
@@ -2392,15 +2392,14 @@ async def kg_query(
     # Build system prompt
     sys_prompt_temp = system_prompt if system_prompt else PROMPTS["rag_response"]
     sys_prompt = sys_prompt_temp.format(
+        user_prompt=f"```\n{query_param.user_prompt}\n```"
+        if query_param.user_prompt
+        else "n/a",
         context_data=context_result.context,
         response_type=query_param.response_type,
     )
 
-    user_query = (
-        "\n\n".join([query, query_param.user_prompt])
-        if query_param.user_prompt
-        else query
-    )
+    user_query = query
 
     if query_param.only_need_prompt:
         prompt_content = "\n\n".join([sys_prompt, "---User Query---", user_query])
@@ -4264,18 +4263,17 @@ async def naive_query(
     if query_param.only_need_context and not query_param.only_need_prompt:
         return QueryResult(content=context_content, raw_data=raw_data)
 
-    user_query = (
-        "\n\n".join([query, query_param.user_prompt])
-        if query_param.user_prompt
-        else query
-    )
-
     sys_prompt_temp = system_prompt if system_prompt else PROMPTS["naive_rag_response"]
     sys_prompt = sys_prompt_temp.format(
+        user_prompt=f"```\n{query_param.user_prompt}\n```"
+        if query_param.user_prompt
+        else "n/a",
         content_data=text_units_str,
         response_type=query_param.response_type,
     )
 
+    user_query = query
+
     if query_param.only_need_prompt:
         prompt_content = "\n\n".join([sys_prompt, "---User Query---", user_query])
         return QueryResult(content=prompt_content, raw_data=raw_data)
diff --git a/lightrag/prompt.py b/lightrag/prompt.py
index 87f12792..c912f340 100644
--- a/lightrag/prompt.py
+++ b/lightrag/prompt.py
@@ -243,6 +243,7 @@ Consider the conversation history if provided to maintain conversational flow an
   - The Document Title in the citation must retain its original language.
   - Output each citation on an individual line
   - Provide maximum of 5 most relevant citations.
+  - Do not generate footnotes section or any text after the references.
 
 5. **Reference Section Example:**
 ```
@@ -252,6 +253,9 @@ Consider the conversation history if provided to maintain conversational flow an
 * [3] Document Title Three
 ```
 
+6. **Additional Instructions**: {user_prompt}
+
+
 ---Source Data---
 Knowledge Graph and Document Chunks:
 
@@ -291,6 +295,7 @@ Consider the conversation history if provided to maintain conversational flow an
   - The Document Title in the citation must retain its original language.
   - Output each citation on an individual line
   - Provide maximum of 5 most relevant citations.
+  - Do not generate footnotes section or any text after the references.
 
 5. **Reference Section Example:**
 ```
@@ -300,6 +305,9 @@ Consider the conversation history if provided to maintain conversational flow an
 * [3] Document Title Three
 ```
 
+6. **Additional Instructions**: {user_prompt}
+
+
 ---Source Data---
 Document Chunks: