From 2ecc10550b1e4757c22c30209159844b2b0a2f6e Mon Sep 17 00:00:00 2001
From: Yaphet Kebede <kebedey@renci.org>
Date: Mon, 15 Dec 2025 10:37:42 -0500
Subject: [PATCH 1/2] out of context issues fix

---
 src/chains/qvkg_chain.py | 70 ++++++++++++++++++++++++++++++++++++++--
 1 file changed, 68 insertions(+), 2 deletions(-)

diff --git a/src/chains/qvkg_chain.py b/src/chains/qvkg_chain.py
index 5201520..3575b57 100644
--- a/src/chains/qvkg_chain.py
+++ b/src/chains/qvkg_chain.py
@@ -25,7 +25,8 @@ def __init__(self, config, default_k=10):
         self.config = config
         self.kg_chain = KGChain(config=config)
         self.qv_chain = QuestionLookupChain(config=config)
-        self.llm = LLMFactory.get_llm(config=config)
+        self.raw_llm = LLMFactory.get_raw_llm(config=config)
+        self.llm = self.raw_llm | LLMFactory.strip_thought
         self.default_lookup_k = default_k
         self.langfuse_client = Langfuse(secret_key=config.LANGFUSE_SECRET_KEY,
                                         public_key=config.LANGFUSE_PUBLIC_KEY,
@@ -112,7 +113,7 @@ def as_generative_chain(self, lookup_parameters=None):
                         "context": x["context"],
                         "chat_history": x["chat_history"],
                         "user_persona": x["user_persona"]
-                    }) | self.COMBINED_ANSWER_PROMPT | self.llm.with_config(name="answer_generation") | StrOutputParser(),
+                    }) | RunnableLambda(self._limit_context_tokens) | self.COMBINED_ANSWER_PROMPT | self.llm.with_config(name="answer_generation") | StrOutputParser(),
                     "extra": RunnableLambda(lambda x: {"knowledge_graph": x["kg_extra"].get("knowledge_graph", {})}),
                     "prompt": RunnableLambda(lambda x: {
                         "input": x["input"],
@@ -149,10 +150,75 @@ def _create_answer_generation_prompt(self, prompt_name):
             MessagesPlaceholder(variable_name="chat_history"),
             ("user", "{input}")
         ])
+
     def _get_raw_from_langfuse(self, prompt_name: str) -> str:
         """Gets raw string for of prompts in langfuse"""
         return self.langfuse_client.get_prompt(prompt_name).prompt
 
+    def _limit_context_tokens(self, inputs: Dict) -> Dict:
+        """
+        Checks the token count of the prompt constructed from inputs.
+        If it exceeds the limit, iteratively removes variables from studies, then studies themselves until it fits.
+        """
+        MAX_TOKENS = 16000  # Leave some buffer for response
+
+        # We need to format the messages to count tokens accurately
+        def get_token_count(current_inputs):
+            messages = self.COMBINED_ANSWER_PROMPT.format_messages(**current_inputs)
+            try:
+                return self.raw_llm.get_num_tokens_from_messages(messages)
+            except Exception:
+                # Fallback if the LLM doesn't support token counting
+                # Rough estimate: 4 chars per token
+                return sum(len(m.content) for m in messages) / 4
+
+        if get_token_count(inputs) <= MAX_TOKENS:
+            return inputs
+
+        # Parse context
+        try:
+            context_str = inputs["context"]
+            # combine_xml_outputs returns <studies>...</studies>
+            root = ET.fromstring(context_str)
+            
+            # Loop until we are under the limit
+            while get_token_count(inputs) > MAX_TOKENS:
+                studies = root.findall('study')
+                if not studies:
+                    break
+                
+                # Check if we have any variables to remove
+                # We want to find the study with the most variables
+                study_with_most_vars = None
+                max_vars = 0
+                
+                for study in studies:
+                    variables_container = study.find('variables')
+                    if variables_container is not None:
+                        vars_in_study = variables_container.findall('variable')
+                        if len(vars_in_study) > max_vars:
+                            max_vars = len(vars_in_study)
+                            study_with_most_vars = study
+                
+                # If we found a study with variables (and count > 0), remove one
+                if study_with_most_vars is not None and max_vars > 0:
+                    variables_container = study_with_most_vars.find('variables')
+                    vars_in_study = variables_container.findall('variable')
+                    # Remove the last variable
+                    variables_container.remove(vars_in_study[-1])
+                else:
+                    # No variables left in any study, remove the last study
+                    root.remove(studies[-1])
+                
+                # Reconstruct context
+                new_context = ET.tostring(root, encoding='unicode')
+                inputs["context"] = new_context
+
+        except ET.ParseError:
+            # If we can't parse, we can't intelligently reduce.
+            pass
+
+        return inputs
 
 
 if __name__ == "__main__":

From 37fe5acd8634d4b7fab16e0997bc9bdb96dfd18d Mon Sep 17 00:00:00 2001
From: Yaphet Kebede <kebedey@renci.org>
Date: Mon, 15 Dec 2025 11:00:30 -0500
Subject: [PATCH 2/2] pin qdrant

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index a36d729..b526954 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,7 +4,7 @@ langchain-community==0.3.18
 httpx==0.27.2
 fastapi==0.115.12
 requests
-qdrant-client
+qdrant-client==1.14.2
 langserve[all]
 pydantic
 langchainhub