Feat: add citation option to agent and enlarge the timeouts. (#9484)

### What problem does this PR solve?

#9422

### Type of change

- [x] New Feature (non-breaking change which adds functionality)

agent/component/agent_with_tools.py

 
         def complete():
             nonlocal hist
-            need2cite = self._canvas.get_reference()["chunks"] and self._id.find("-->") < 0
+            need2cite = self._param.cite and self._canvas.get_reference()["chunks"] and self._id.find("-->") < 0
             cited = False
             if hist[0]["role"] == "system" and need2cite:
                 if len(hist) < 7:

agent/component/llm.py

         prompt = self.string_format(prompt, args)
         for m in msg:
             m["content"] = self.string_format(m["content"], args)
-        if self._canvas.get_reference()["chunks"]:
+        if self._param.cite and self._canvas.get_reference()["chunks"]:
             prompt += citation_prompt()
 
         return prompt, msg

graphrag/entity_resolution.py

             nonlocal remain_candidates_to_resolve, callback
             async with semaphore:
                 try:
-                    with trio.move_on_after(180) as cancel_scope:
+                    with trio.move_on_after(280) as cancel_scope:
                         await self._resolve_candidate(candidate_batch, result_set, result_lock)
                         remain_candidates_to_resolve = remain_candidates_to_resolve - len(candidate_batch[1])
                         callback(msg=f"Resolved {len(candidate_batch[1])} pairs, {remain_candidates_to_resolve} are remained to resolve. ")
         logging.info(f"Created resolution prompt {len(text)} bytes for {len(candidate_resolution_i[1])} entity pairs of type {candidate_resolution_i[0]}")
         async with chat_limiter:
             try:
-                with trio.move_on_after(120) as cancel_scope:
+                with trio.move_on_after(240) as cancel_scope:
                     response = await trio.to_thread.run_sync(self._chat, text, [{"role": "user", "content": "Output:"}], {})
                 if cancel_scope.cancelled_caught:
                     logging.warning("_resolve_candidate._chat timeout, skipping...")

graphrag/general/community_reports_extractor.py

             text = perform_variable_replacements(self._extraction_prompt, variables=prompt_variables)
             async with chat_limiter:
                 try:
-                    with trio.move_on_after(80) as cancel_scope:
+                    with trio.move_on_after(180) as cancel_scope:
                         response = await trio.to_thread.run_sync( self._chat, text, [{"role": "user", "content": "Output:"}], {})
                     if cancel_scope.cancelled_caught:
                         logging.warning("extract_community_report._chat timeout, skipping...")

graphrag/general/index.py

     ):
         chunks.append(d["content_with_weight"])
 
-    subgraph = await generate_subgraph(
-        LightKGExt
-        if "method" not in row["kb_parser_config"].get("graphrag", {}) or row["kb_parser_config"]["graphrag"]["method"] != "general"
-        else GeneralKGExt,
-        tenant_id,
-        kb_id,
-        doc_id,
-        chunks,
-        language,
-        row["kb_parser_config"]["graphrag"].get("entity_types", []),
-        chat_model,
-        embedding_model,
-        callback,
-    )
+    with trio.fail_after(len(chunks)*60):
+        subgraph = await generate_subgraph(
+            LightKGExt
+            if "method" not in row["kb_parser_config"].get("graphrag", {}) or row["kb_parser_config"]["graphrag"]["method"] != "general"
+            else GeneralKGExt,
+            tenant_id,
+            kb_id,
+            doc_id,
+            chunks,
+            language,
+            row["kb_parser_config"]["graphrag"].get("entity_types", []),
+            chat_model,
+            embedding_model,
+            callback,
+        )
+
     if not subgraph:
         return
 
     return
 
 
-@timeout(60*60, 1)
 async def generate_subgraph(
     extractor: Extractor,
     tenant_id: str,

rag/svr/task_executor.py

     return res, tk_count
 
 
-@timeout(60*60, 1)
+@timeout(60*60*2, 1)
 async def do_handle_task(task):
     task_id = task["id"]
     task_from_page = task["from_page"]