aiagents4pharma 1.27.2__tar.gz → 1.29.0__tar.gz

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.27.2
+Version: 1.29.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -91,6 +91,7 @@ Our toolkit currently consists of the following agents:
 ![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
 
 ### Installation
+
 _Please use version 1.26.2 or later for better support with NVIDIA NIM models._
 
 #### Option 1: PyPI
@@ -135,10 +136,10 @@ cd AIAgents4Pharma/aiagents4pharma/talk2knowledgegraphs
    LANGCHAIN_TRACING_V2=true
    LANGCHAIN_API_KEY=your_langchain_api_key_here
    # Notes:
-   # - The API endpoint for Ollama is already set in env.example.
-   # - Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma.
-   # - If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed.
-   # - Langsmith API for tracing is optional for both, set it in env.example if required.
+   # The API endpoint for Ollama is already set in env.example.
+   # Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma.
+   # If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed.
+   # Langsmith API for tracing is optional for both, set it in env.example if required.
    ```
 
 4. Save the file.

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/README.md

@@ -26,6 +26,7 @@ Our toolkit currently consists of the following agents:
 ![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
 
 ### Installation
+
 _Please use version 1.26.2 or later for better support with NVIDIA NIM models._
 
 #### Option 1: PyPI
@@ -70,10 +71,10 @@ cd AIAgents4Pharma/aiagents4pharma/talk2knowledgegraphs
    LANGCHAIN_TRACING_V2=true
    LANGCHAIN_API_KEY=your_langchain_api_key_here
    # Notes:
-   # - The API endpoint for Ollama is already set in env.example.
-   # - Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma.
-   # - If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed.
-   # - Langsmith API for tracing is optional for both, set it in env.example if required.
+   # The API endpoint for Ollama is already set in env.example.
+   # Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma.
+   # If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed.
+   # Langsmith API for tracing is optional for both, set it in env.example if required.
    ```
 
 4. Save the file.

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/agents/__init__.py

@@ -5,3 +5,4 @@ This file is used to import all the modules in the package.
 from . import main_agent
 from . import s2_agent
 from . import zotero_agent
+from . import pdf_agent

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/agents/main_agent.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+
+"""
+Main agent for the talk2scholars app using ReAct pattern.
+
+This module implements a hierarchical agent system where a supervisor agent
+routes queries to specialized sub-agents. It follows the LangGraph patterns
+for multi-agent systems and implements proper state management.
+"""
+
+import logging
+import hydra
+from langgraph_supervisor import create_supervisor
+from langchain_openai import ChatOpenAI
+from langchain_core.language_models.chat_models import BaseChatModel
+from langgraph.checkpoint.memory import MemorySaver
+from ..agents.s2_agent import get_app as get_app_s2
+from ..agents.zotero_agent import get_app as get_app_zotero
+from ..state.state_talk2scholars import Talk2Scholars
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def get_app(uniq_id, llm_model: BaseChatModel):
+    """
+    Initializes and returns the LangGraph-based hierarchical agent system.
+
+    This function constructs the agent workflow by defining nodes for the supervisor
+    and sub-agents. It compiles the graph using `StateGraph` to enable structured
+    conversational workflows.
+
+    Args:
+        thread_id (str): A unique session identifier for tracking conversation state.
+        llm_model (BaseChatModel, optional): The language model used for query processing.
+            Defaults to `ChatOpenAI(model="gpt-4o-mini", temperature=0)`.
+
+    Returns:
+        StateGraph: A compiled LangGraph application that can process user queries.
+
+    Example:
+        >>> app = get_app("thread_123")
+        >>> result = app.invoke(initial_state)
+    """
+    if llm_model.model_name == "gpt-4o-mini":
+        llm_model = ChatOpenAI(
+            model="gpt-4o-mini",
+            temperature=0,
+            model_kwargs={"parallel_tool_calls": False},
+        )
+    # Load hydra configuration
+    logger.log(logging.INFO, "Launching Talk2Scholars with thread_id %s", uniq_id)
+    with hydra.initialize(version_base=None, config_path="../configs/"):
+        cfg = hydra.compose(
+            config_name="config", overrides=["agents/talk2scholars/main_agent=default"]
+        )
+        cfg = cfg.agents.talk2scholars.main_agent
+    logger.log(logging.INFO, "System_prompt of Talk2Scholars: %s", cfg.system_prompt)
+    # Create supervisor workflow
+    workflow = create_supervisor(
+        [
+            get_app_s2(uniq_id, llm_model),  # semantic scholar
+            get_app_zotero(uniq_id, llm_model),  # zotero
+        ],
+        model=llm_model,
+        state_schema=Talk2Scholars,
+        # Full history is needed to extract
+        # the tool artifacts
+        output_mode="full_history",
+        add_handoff_back_messages=False,
+        prompt=cfg.system_prompt,
+    )
+
+    # Compile and run
+    app = workflow.compile(checkpointer=MemorySaver(), name="Talk2Scholars_MainAgent")
+
+    return app

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/agents/pdf_agent.py

@@ -0,0 +1,106 @@
+#!/usr/bin/env python3
+"""
+Agent for interacting with PDF documents via question and answer.
+
+This module initializes and compiles a LangGraph application that enables users to query PDF
+documents using a question_and_answer tool. It integrates a language model and follows
+the ReAct pattern to process and answer queries related to PDF content.
+
+Usage:
+    >>> app = get_app("unique_thread_id")
+    >>> response = app.invoke(initial_state)
+"""
+
+import logging
+import hydra
+from langchain_core.language_models.chat_models import BaseChatModel
+from langgraph.graph import START, StateGraph
+from langgraph.prebuilt import create_react_agent, ToolNode
+from langgraph.checkpoint.memory import MemorySaver
+from ..state.state_talk2scholars import Talk2Scholars
+from ..tools.pdf.question_and_answer import question_and_answer_tool
+from ..tools.s2.query_results import query_results
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def get_app(
+    uniq_id,
+    llm_model: BaseChatModel
+):
+    """
+    Initializes and returns the LangGraph application for the PDF agent.
+
+    This function sets up the PDF agent by loading configuration settings via Hydra,
+    initializing a model, and creating a workflow graph that incorporates
+    PDF-specific tools. The agent is built using the ReAct pattern to facilitate interactive
+    querying and processing of PDF documents.
+
+    Args:
+        uniq_id (str): A unique identifier for the current conversation session or thread.
+        llm_model (BaseChatModel, optional): The language model instance to be used. 
+            Defaults to ChatOpenAI(model="gpt-4o-mini", temperature=0).
+
+    Returns:
+        StateGraph: A compiled LangGraph application capable of handling PDF interactions.
+
+    Example:
+        >>> app = get_app("thread_123")
+        >>> result = app.invoke(initial_state)
+    """
+    # Load configuration using Hydra.
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(
+            config_name="config",
+            overrides=["agents/talk2scholars/pdf_agent=default"],
+        )
+        cfg = cfg.agents.talk2scholars.pdf_agent
+        logger.info("Loaded pdf_agent configuration.")
+
+    def agent_pdf_node(state: Talk2Scholars):
+        """
+        Processes the current state by invoking the language model for PDF question and answer.
+
+        Args:
+            state (Talk2Scholars): The current conversation state containing query details
+            and context.
+
+        Returns:
+            Any: The response generated by the language model after processing the state.
+        """
+        logger.info("Creating Agent_PDF node with thread_id %s", uniq_id)
+        response = model.invoke(
+            state,
+            {"configurable": {"thread_id": uniq_id}}
+        )
+        return response
+
+    # Define the tool node that includes the PDF QnA tool.
+    tools = ToolNode([question_and_answer_tool, query_results])
+
+    logger.info("Using OpenAI model %s", llm_model)
+
+    # Create the agent using the provided BaseChatModel instance.
+    model = create_react_agent(
+        llm_model,
+        tools=tools,
+        state_schema=Talk2Scholars,
+        prompt=cfg.pdf_agent,
+        checkpointer=MemorySaver(),
+    )
+
+    # Define a new workflow graph with the state schema.
+    workflow = StateGraph(Talk2Scholars)
+    workflow.add_node("agent_pdf", agent_pdf_node)
+    workflow.add_edge(START, "agent_pdf")
+
+    # Initialize memory to persist state between runs.
+    checkpointer = MemorySaver()
+
+    # Compile the graph into a runnable app.
+    app = workflow.compile(checkpointer=checkpointer)
+    logger.info("Compiled the PDF agent graph.")
+
+    return app

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/agents/s2_agent.py

@@ -28,9 +28,7 @@ logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 
-def get_app(
-    uniq_id, llm_model: BaseChatModel
-):
+def get_app(uniq_id, llm_model: BaseChatModel):
     """
     Initializes and returns the LangGraph application for the Semantic Scholar (S2) agent.
 
@@ -86,6 +84,7 @@ def get_app(
             config_name="config", overrides=["agents/talk2scholars/s2_agent=default"]
         )
         cfg = cfg.agents.talk2scholars.s2_agent
+        logger.log(logging.INFO, "Loaded configuration for S2 agent")
 
     # Define the tools
     tools = ToolNode(
@@ -107,7 +106,7 @@ def get_app(
         llm_model,
         tools=tools,
         state_schema=Talk2Scholars,
-        state_modifier=cfg.s2_agent,
+        prompt=cfg.s2_agent,
         checkpointer=MemorySaver(),
     )
 
@@ -122,7 +121,12 @@ def get_app(
     # This compiles it into a LangChain Runnable,
     # meaning you can use it as you would any other runnable.
     # Note that we're (optionally) passing the memory when compiling the graph
-    app = workflow.compile(checkpointer=checkpointer)
-    logger.log(logging.INFO, "Compiled the graph")
+    app = workflow.compile(checkpointer=checkpointer, name="agent_s2")
+    logger.log(
+        logging.INFO,
+        "Compiled the graph with thread_id %s and llm_model %s",
+        uniq_id,
+        llm_model,
+    )
 
     return app

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/agents/zotero_agent.py

@@ -14,6 +14,7 @@ from langgraph.prebuilt import create_react_agent, ToolNode
 from langgraph.checkpoint.memory import MemorySaver
 from ..state.state_talk2scholars import Talk2Scholars
 from ..tools.zotero.zotero_read import zotero_search_tool
+from ..tools.zotero.zotero_write import zotero_save_tool
 from ..tools.s2.display_results import display_results as s2_display
 from ..tools.s2.query_results import query_results as s2_query_results
 from ..tools.s2.retrieve_semantic_scholar_paper_id import (
@@ -25,9 +26,7 @@ logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 
-def get_app(
-    uniq_id, llm_model: BaseChatModel
-):
+def get_app(uniq_id, llm_model: BaseChatModel):
     """
     Initializes and returns the LangGraph application for the Zotero agent.
 
@@ -83,6 +82,7 @@ def get_app(
             overrides=["agents/talk2scholars/zotero_agent=default"],
         )
         cfg = cfg.agents.talk2scholars.zotero_agent
+        logger.log(logging.INFO, "Loaded configuration for Zotero agent")
 
     # Define the tools
     tools = ToolNode(
@@ -91,6 +91,7 @@ def get_app(
             s2_display,
             s2_query_results,
             retrieve_semantic_scholar_paper_id,
+            zotero_save_tool,
         ]
     )
 
@@ -102,7 +103,7 @@ def get_app(
         llm_model,
         tools=tools,
         state_schema=Talk2Scholars,
-        state_modifier=cfg.zotero_agent,
+        prompt=cfg.zotero_agent,
         checkpointer=MemorySaver(),
     )
 
@@ -114,7 +115,12 @@ def get_app(
     checkpointer = MemorySaver()
 
     # Compile the graph
-    app = workflow.compile(checkpointer=checkpointer)
-    logger.log(logging.INFO, "Compiled the graph")
+    app = workflow.compile(checkpointer=checkpointer, name="agent_zotero")
+    logger.log(
+        logging.INFO,
+        "Compiled the graph with thread_id %s and llm_model %s",
+        uniq_id,
+        llm_model,
+    )
 
     return app

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py

@@ -4,4 +4,5 @@ Import all the modules in the package
 
 from . import s2_agent
 from . import main_agent
+from . import pdf_agent
 from . import zotero_agent

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml

@@ -0,0 +1,13 @@
+_target_: agents.main_agent.get_app
+temperature: 0
+system_prompt: >
+  You are the Talk2Scholars agent coordinating academic paper discovery and analysis.
+
+  You have access to the following agents:
+  1. S2_agent: This agent can be used to search and recommend papers
+     from Semantic Scholar. Use this agent when the user asks for
+     general paper searches and recommendations.
+  2. Zotero_agent: This agent can be used to retrieve, display, and query
+     papers from the Zotero library. Use this agent only when the user
+     explicitly asks for papers from Zotero. This tool can also be used to
+     save papers in under collections in the zotero library

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml

@@ -0,0 +1,19 @@
+_target_: agents.s2_agent.get_app
+s2_agent: >
+  You are an academic research assistant with access to the
+  Semantic Scholar API for paper discovery and analysis.
+
+  AVAILABLE TOOLS:
+  1. search - Search for academic papers by query string
+  2. display_results - Display the papers retrieved by other tools
+  3. single_paper_rec - Get recommendations based on a SINGLE paper
+  4. multi_paper_rec - Get recommendations based on MULTIPLE papers
+  5. query_results - Ask questions about the current set of papers
+  6. retrieve_semantic_scholar_paper_id - Get Semantic Scholar ID for a paper title
+
+  WORKFLOW STEPS:
+  1. When user requests papers, use search/recommendation tools to find papers
+  2. Use `display_results` tool to display the response from the search/recommendation tools 
+  3. Use `query_results` tool to query over the selected paper only when the user asks to
+  4. When the user wants recommendations, you can get the "paper_id" using `query_results` tool in the "last_displayed_results" key, then
+     pass the "paper_id" to `search`, `single_paper_rec` or `multi_paper_rec` tools depending on the user's query. Do not use "arxiv_id"

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml

@@ -0,0 +1,19 @@
+target: agents.zotero_agent.get_app
+zotero_agent: >
+  You are a specialized Zotero library agent with access to tools for paper retrieval and management.
+
+  AVAILABLE TOOLS:
+  1. zotero_search_tool - Search and retrieve papers from Zotero library
+  2. display_results - Display the papers retrieved by other tools
+  3. query_results - Ask questions about the current set of papers
+  4. retrieve_semantic_scholar_paper_id - Get Semantic Scholar ID for a paper title for the papers from zotero library
+  5. zotero_write - Save paper to users zotero library under specfied collections
+
+
+  WORKFLOW STEPS
+  1. When user requests papers, use `zotero_search_tool` to find papers
+  2. Use `display_results` tool to display the response
+  3. Use `query_results` tool to query over the selected paper only when the user asks to
+  4. Use `retrieve_semantic_scholar_paper_id` to get the semantic scholar id of a paper title for the papers from zotero library
+  5. Use `zotero_write` to save the papers to users zotero library under collections and call `display_results` only after you recive
+     the save was successfull

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/configs/config.yaml

@@ -4,8 +4,11 @@ defaults:
   - agents/talk2scholars/s2_agent: default
   - agents/talk2scholars/zotero_agent: default
   - app/frontend: default
+  - agents/talk2scholars/pdf_agent: default
   - tools/search: default
   - tools/single_paper_recommendation: default
   - tools/multi_paper_recommendation: default
   - tools/retrieve_semantic_scholar_paper_id: default
+  - tools/question_and_answer: default
   - tools/zotero_read: default
+  - tools/zotero_write: default

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/configs/tools/__init__.py

@@ -5,4 +5,6 @@ Import all the modules in the package
 from . import search
 from . import single_paper_recommendation
 from . import multi_paper_recommendation
+from . import question_and_answer
 from . import zotero_read
+from . import zotero_write

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml

@@ -9,8 +9,8 @@ api_fields:
   - "authors"
   - "citationCount"
   - "url"
+  - "externalIds"
 # Commented fields that could be added later if needed
-# - "externalIds"
 
 # Default headers and params
 headers:

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/configs/tools/search/default.yaml

@@ -9,8 +9,8 @@ api_fields:
   - "authors"
   - "citationCount"
   - "url"
+  - "externalIds"
 # Commented fields that could be added later if needed
-# - "externalIds"
 #  - "publicationTypes"
 #  - "openAccessPdf"
 

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py

@@ -0,0 +1,3 @@
+"""
+Import all the modules in the package
+"""

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml

@@ -9,8 +9,8 @@ api_fields:
   - "authors"
   - "citationCount"
   - "url"
+  - "externalIds"
 # Commented fields that could be added later if needed
-# - "externalIds"
 #  - "publicationTypes"
 #  - "openAccessPdf"
 

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/configs/tools/zotero_read/__init__.py

@@ -0,0 +1,3 @@
+"""
+Import all the modules in the package
+"""

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml

@@ -0,0 +1,56 @@
+# Default configuration for Zotero search tool
+library_type: "user" # Type of library ('user' or 'group')
+default_limit: 2
+request_timeout: 10
+user_id: ${oc.env:ZOTERO_USER_ID} # Load from environment variable
+api_key: ${oc.env:ZOTERO_API_KEY} # Load from environment variable
+
+# Default search parameters
+search_params:
+  limit: ${.default_limit}
+
+# Item Types and Limit
+zotero:
+  max_limit: 100
+  filter_item_types:
+    [
+      "Artwork",
+      "Audio Recording",
+      "Bill",
+      "Blog Post",
+      "Book",
+      "Book Section",
+      "Case",
+      "Conference Paper",
+      "Dataset",
+      "Dictionary Entry",
+      "Document",
+      "E-mail",
+      "Encyclopedia Article",
+      "Film",
+      "Forum Post",
+      "Hearing",
+      "Instant Message",
+      "Interview",
+      "Journal Article",
+      "Letter",
+      "Magazine Article",
+      "Manuscript",
+      "Map",
+      "Newspaper Article",
+      "Patent",
+      "Podcast",
+      "Preprint",
+      "Presentation",
+      "Radio Broadcast",
+      "Report",
+      "Software",
+      "Standard",
+      "Statute",
+      "Thesis",
+      "TV Broadcast",
+      "Video Recording",
+      "Web Page",
+    ]
+
+  filter_excluded_types: ["attachment", "note", "annotation"]

aiagents4pharma-1.29.0/aiagents4pharma/talk2scholars/configs/tools/zotero_write/__inti__.py

@@ -0,0 +1,3 @@
+"""
+Import all the modules in the package
+"""

{aiagents4pharma-1.27.2 → aiagents4pharma-1.29.0}/aiagents4pharma/talk2scholars/state/state_talk2scholars.py

@@ -60,5 +60,6 @@ class Talk2Scholars(AgentState):
     last_displayed_papers: Annotated[Dict[str, Any], replace_dict]
     papers: Annotated[Dict[str, Any], replace_dict]
     multi_papers: Annotated[Dict[str, Any], replace_dict]
+    pdf_data: Annotated[Dict[str, Any], replace_dict]
     zotero_read: Annotated[Dict[str, Any], replace_dict]
     llm_model: BaseChatModel