aiagents4pharma 0.0.0__py3-none-any.whl

aiagents4pharma/talk2biomodels/states/__init__.py

@@ -0,0 +1,6 @@
+"""
+This file is used to import all the modules in the package.
+"""
+
+# import everything from the module
+from . import state_talk2biomodels

aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+
+"""
+This is the state file for the Talk2BioModels agent.
+"""
+
+import operator
+from typing import Annotated
+
+from langchain_core.embeddings import Embeddings
+from langchain_core.language_models import BaseChatModel
+from langgraph.prebuilt.chat_agent_executor import AgentState
+
+
+def add_data(data1: dict, data2: dict) -> dict:
+    """
+    A reducer function to merge two dictionaries.
+    """
+    left_idx_by_name = {data["name"]: idx for idx, data in enumerate(data1)}
+    merged = data1.copy()
+    for data in data2:
+        idx = left_idx_by_name.get(data["name"])
+        if idx is not None:
+            merged[idx] = data
+        else:
+            merged.append(data)
+    return merged
+
+
+class Talk2Biomodels(AgentState):
+    """
+    The state for the Talk2BioModels agent.
+    """
+
+    llm_model: BaseChatModel
+    text_embedding_model: Embeddings
+    pdf_file_name: str
+    # A StateGraph may receive a concurrent updates
+    # which is not supported by the StateGraph. Hence,
+    # we need to add a reducer function to handle the
+    # concurrent updates.
+    # https://langchain-ai.github.io/langgraph/troubleshooting/errors/INVALID_CONCURRENT_GRAPH_UPDATE/
+    model_id: Annotated[list, operator.add]
+    sbml_file_path: Annotated[list, operator.add]
+    model_as_string: Annotated[list, operator.add]
+    dic_simulated_data: Annotated[list[dict], add_data]
+    dic_scanned_data: Annotated[list[dict], add_data]
+    dic_steady_state_data: Annotated[list[dict], add_data]
+    dic_annotations_data: Annotated[list[dict], add_data]