aiagents4pharma 1.22.4__tar.gz → 1.23.0__tar.gz

{aiagents4pharma-1.22.4 → aiagents4pharma-1.23.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.22.4
+Version: 1.23.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -36,6 +36,7 @@ Requires-Dist: pylint==3.3.1
 Requires-Dist: pypdf==5.2.0
 Requires-Dist: pytest==8.3.3
 Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: pyzotero==1.6.9
 Requires-Dist: streamlit==1.39.0
 Requires-Dist: sentence_transformers==3.3.1
 Requires-Dist: tabulate==0.9.0
@@ -59,7 +60,6 @@ Requires-Dist: streamlit-feedback
 ![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)
 ![Docker Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?link=https%3A%2F%2Fhub.docker.com%2Frepository%2Fdocker%2Fvirtualpatientengine%2Ftalk2biomodels%2Fgeneral)
 
-
 ## Introduction
 
 Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
@@ -99,8 +99,8 @@ _Please note that this option is currently available only for Talk2Biomodels._
    ```
    docker run -e OPENAI_API_KEY=<openai_api_key> -e NVIDIA_API_KEY=<nvidia_api_key> -p 8501:8501 virtualpatientengine/talk2biomodels
    ```
-_You can create a free account at NVIDIA and apply for their
-free credits [here](https://build.nvidia.com/explore/discover)._
+   _You can create a free account at NVIDIA and apply for their
+   free credits [here](https://build.nvidia.com/explore/discover)._
 
 #### Option 3: git
 
@@ -114,31 +114,43 @@ free credits [here](https://build.nvidia.com/explore/discover)._
    pip install -r requirements.txt
    ```
 3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
+
    ```bash
    export OPENAI_API_KEY=....
    ```
+
    ```bash
    export NVIDIA_API_KEY=....
    ```
-_You can create a free account at NVIDIA and apply for their
-free credits [here](https://build.nvidia.com/explore/discover)._
 
-4. **[Optional] Initialize LANGSMITH_API_KEY**
+   _You can create a free account at NVIDIA and apply for their
+   free credits [here](https://build.nvidia.com/explore/discover)._
+
+4. **Initialize ZOTERO_API_KEY and ZOTERO_USER_ID**
+
+   ```bash
+   export ZOTERO_API_KEY=....
+   export ZOTERO_USER_ID=....
+   ```
+
+5. **[Optional] Initialize LANGSMITH_API_KEY**
+
    ```bash
    export LANGCHAIN_TRACING_V2=true
    export LANGCHAIN_API_KEY=<your-api-key>
    ```
-_Please note that this will create a new tracing project in your Langsmith
-account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
-`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
-default to the name `default`. `xxxx` will be the 4-digit ID created for the
-session._
 
-5. **Launch the app:**
+   _Please note that this will create a new tracing project in your Langsmith
+   account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
+   `KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+   default to the name `default`. `xxxx` will be the 4-digit ID created for the
+   session._
+
+6. **Launch the app:**
    ```bash
    streamlit run app/frontend/streamlit_app_<agent>.py
    ```
-_Replace <agent> with the agent name you are interested to launch._
+   _Replace <agent> with the agent name you are interested to launch._
 
 For detailed instructions on each agent, please refer to their respective modules.
 

{aiagents4pharma-1.22.4 → aiagents4pharma-1.23.0}/README.md

@@ -6,7 +6,6 @@
 ![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)
 ![Docker Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?link=https%3A%2F%2Fhub.docker.com%2Frepository%2Fdocker%2Fvirtualpatientengine%2Ftalk2biomodels%2Fgeneral)
 
-
 ## Introduction
 
 Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
@@ -46,8 +45,8 @@ _Please note that this option is currently available only for Talk2Biomodels._
    ```
    docker run -e OPENAI_API_KEY=<openai_api_key> -e NVIDIA_API_KEY=<nvidia_api_key> -p 8501:8501 virtualpatientengine/talk2biomodels
    ```
-_You can create a free account at NVIDIA and apply for their
-free credits [here](https://build.nvidia.com/explore/discover)._
+   _You can create a free account at NVIDIA and apply for their
+   free credits [here](https://build.nvidia.com/explore/discover)._
 
 #### Option 3: git
 
@@ -61,31 +60,43 @@ free credits [here](https://build.nvidia.com/explore/discover)._
    pip install -r requirements.txt
    ```
 3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
+
    ```bash
    export OPENAI_API_KEY=....
    ```
+
    ```bash
    export NVIDIA_API_KEY=....
    ```
-_You can create a free account at NVIDIA and apply for their
-free credits [here](https://build.nvidia.com/explore/discover)._
 
-4. **[Optional] Initialize LANGSMITH_API_KEY**
+   _You can create a free account at NVIDIA and apply for their
+   free credits [here](https://build.nvidia.com/explore/discover)._
+
+4. **Initialize ZOTERO_API_KEY and ZOTERO_USER_ID**
+
+   ```bash
+   export ZOTERO_API_KEY=....
+   export ZOTERO_USER_ID=....
+   ```
+
+5. **[Optional] Initialize LANGSMITH_API_KEY**
+
    ```bash
    export LANGCHAIN_TRACING_V2=true
    export LANGCHAIN_API_KEY=<your-api-key>
    ```
-_Please note that this will create a new tracing project in your Langsmith
-account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
-`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
-default to the name `default`. `xxxx` will be the 4-digit ID created for the
-session._
 
-5. **Launch the app:**
+   _Please note that this will create a new tracing project in your Langsmith
+   account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
+   `KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
+   default to the name `default`. `xxxx` will be the 4-digit ID created for the
+   session._
+
+6. **Launch the app:**
    ```bash
    streamlit run app/frontend/streamlit_app_<agent>.py
    ```
-_Replace <agent> with the agent name you are interested to launch._
+   _Replace <agent> with the agent name you are interested to launch._
 
 For detailed instructions on each agent, please refer to their respective modules.
 

{aiagents4pharma-1.22.4 → aiagents4pharma-1.23.0}/aiagents4pharma/talk2scholars/agents/__init__.py

@@ -1,6 +1,7 @@
-'''
+"""
 This file is used to import all the modules in the package.
-'''
+"""
 
 from . import main_agent
 from . import s2_agent
+from . import zotero_agent

{aiagents4pharma-1.22.4 → aiagents4pharma-1.23.0}/aiagents4pharma/talk2scholars/agents/main_agent.py

@@ -19,6 +19,7 @@ from langgraph.checkpoint.memory import MemorySaver
 from langgraph.graph import END, START, StateGraph
 from langgraph.types import Command
 from ..agents import s2_agent
+from ..agents import zotero_agent
 from ..state.state_talk2scholars import Talk2Scholars
 
 # Configure logging
@@ -49,7 +50,7 @@ def make_supervisor_node(llm_model: BaseChatModel, thread_id: str) -> Callable:
 
     This function initializes the routing logic by leveraging the system and router prompts defined
     in the Hydra configuration. The supervisor determines whether to
-    call a sub-agent (like `s2_agent`)
+    call a sub-agent (like `s2_agent`, `zotero_agent`)
     or directly generate a response using the language model.
 
     Args:
@@ -62,12 +63,12 @@ def make_supervisor_node(llm_model: BaseChatModel, thread_id: str) -> Callable:
     """
     cfg = get_hydra_config()
     logger.info("Hydra configuration for Talk2Scholars main agent loaded: %s", cfg)
-    members = ["s2_agent"]
+    members = ["s2_agent", "zotero_agent"]
     options = ["FINISH"] + members
     # Define system prompt for general interactions
     system_prompt = cfg.system_prompt
     # Define router prompt for routing to sub-agents
-    router_prompt = cfg.router_prompt
+    router_prompt = cfg.router_prompt + " " + " ".join(members)
 
     class Router(BaseModel):
         """Worker to route to next. If no workers needed, route to FINISH."""
@@ -90,7 +91,7 @@ def make_supervisor_node(llm_model: BaseChatModel, thread_id: str) -> Callable:
         Returns:
             Command: A command dictating whether to invoke a sub-agent or generate a final response.
         """
-        messages = [SystemMessage(content=router_prompt)] + state["messages"]
+        messages = [SystemMessage(content=router_prompt)] + list(state["messages"])
         structured_llm = llm_model.with_structured_output(Router)
         response = structured_llm.invoke(messages)
         goto = response.next
@@ -189,6 +190,51 @@ def get_app(
             goto="supervisor",
         )
 
+    def call_zotero_agent(
+        state: Talk2Scholars,
+    ) -> Command[Literal["supervisor"]]:
+        """
+        Invokes the Zotero agent to retrieve and process papers from the user's Zotero library.
+
+        This function calls the Zotero agent, which interacts with the user's Zotero database
+        to retrieve relevant papers based on the conversation context. It updates the
+        conversation state with the retrieved papers and relevant metadata.
+
+        Args:
+            state (Talk2Scholars): The current conversation state, containing user messages
+                and any previously retrieved Zotero data.
+
+        Returns:
+            Command: A command that updates the conversation state with retrieved Zotero
+                papers and metadata before returning control to the supervisor node.
+
+        Example:
+            >>> result = call_zotero_agent(current_state)
+            >>> next_step = result.goto
+        """
+        logger.info("Calling Zotero agent")
+        app = zotero_agent.get_app(thread_id, llm_model)
+        # Invoke the Zotero agent, passing state
+        response = app.invoke(
+            state,
+            {
+                "configurable": {
+                    "config_id": thread_id,
+                    "thread_id": thread_id,
+                }
+            },
+        )
+        logger.info("Zotero agent completed with response")
+        return Command(
+            update={
+                "messages": response["messages"],
+                "zotero_read": response.get("zotero_read", {}),
+                "last_displayed_papers": response.get("last_displayed_papers", {}),
+            },
+            # Always return to supervisor
+            goto="supervisor",
+        )
+
     # Initialize LLM
     logger.info("Using model %s with temperature %s", llm_model, cfg.temperature)
 
@@ -198,6 +244,7 @@ def get_app(
     # Add nodes
     workflow.add_node("supervisor", supervisor)
     workflow.add_node("s2_agent", call_s2_agent)
+    workflow.add_node("zotero_agent", call_zotero_agent)
     # Add edges
     workflow.add_edge(START, "supervisor")
     # Compile the workflow

aiagents4pharma-1.23.0/aiagents4pharma/talk2scholars/agents/zotero_agent.py

@@ -0,0 +1,120 @@
+#!/usr/bin/env python3
+
+"""
+Agent for interacting with Zotero
+"""
+
+import logging
+from typing import Any, Dict
+import hydra
+from langchain_openai import ChatOpenAI
+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.zotero.zotero_read import zotero_search_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 (
+    retrieve_semantic_scholar_paper_id,
+)
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def get_app(
+    uniq_id, llm_model: BaseChatModel = ChatOpenAI(model="gpt-4o-mini", temperature=0)
+):
+    """
+    Initializes and returns the LangGraph application for the Zotero agent.
+
+    This function sets up the Zotero agent, which integrates various tools to search,
+    retrieve, and display research papers from Zotero. The agent follows the ReAct
+    pattern for structured interaction.
+
+    Args:
+        uniq_id (str): Unique identifier for the current conversation session.
+        llm_model (BaseChatModel, optional): The language model to be used by the agent.
+            Defaults to `ChatOpenAI(model="gpt-4o-mini", temperature=0)`.
+
+    Returns:
+        StateGraph: A compiled LangGraph application that enables the Zotero agent to
+            process user queries and retrieve research papers.
+
+    Example:
+        >>> app = get_app("thread_123")
+        >>> result = app.invoke(initial_state)
+    """
+
+    def agent_zotero_node(state: Talk2Scholars) -> Dict[str, Any]:
+        """
+        Processes the user query and retrieves relevant research papers from Zotero.
+
+        This function calls the language model using the configured `ReAct` agent to
+        analyze the state and generate an appropriate response. The function then
+        returns control to the main supervisor.
+
+        Args:
+            state (Talk2Scholars): The current conversation state, including messages exchanged
+                and any previously retrieved research papers.
+
+        Returns:
+            Dict[str, Any]: A dictionary containing the updated conversation state.
+
+        Example:
+            >>> result = agent_zotero_node(current_state)
+            >>> papers = result.get("papers", [])
+        """
+        logger.log(
+            logging.INFO, "Creating Agent_Zotero node with thread_id %s", uniq_id
+        )
+        result = model.invoke(state, {"configurable": {"thread_id": uniq_id}})
+
+        return result
+
+    # Load hydra configuration
+    logger.log(logging.INFO, "Load Hydra configuration for Talk2Scholars Zotero agent.")
+    with hydra.initialize(version_base=None, config_path="../configs"):
+        cfg = hydra.compose(
+            config_name="config",
+            overrides=["agents/talk2scholars/zotero_agent=default"],
+        )
+        cfg = cfg.agents.talk2scholars.zotero_agent
+
+    # Define the tools
+    tools = ToolNode(
+        [
+            zotero_search_tool,
+            s2_display,
+            s2_query_results,
+            retrieve_semantic_scholar_paper_id,
+        ]
+    )
+
+    # Define the model
+    logger.log(logging.INFO, "Using model %s", llm_model)
+
+    # Create the agent
+    model = create_react_agent(
+        llm_model,
+        tools=tools,
+        state_schema=Talk2Scholars,
+        state_modifier=cfg.zotero_agent,
+        checkpointer=MemorySaver(),
+    )
+
+    workflow = StateGraph(Talk2Scholars)
+    workflow.add_node("agent_zotero", agent_zotero_node)
+    workflow.add_edge(START, "agent_zotero")
+
+    # Initialize memory to persist state between graph runs
+    checkpointer = MemorySaver()
+
+    # Compile the graph
+    app = workflow.compile(checkpointer=checkpointer)
+    logger.log(logging.INFO, "Compiled the graph")
+
+    return app

{aiagents4pharma-1.22.4 → aiagents4pharma-1.23.0}/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py

@@ -4,3 +4,4 @@ Import all the modules in the package
 
 from . import s2_agent
 from . import main_agent
+from . import zotero_agent

aiagents4pharma-1.23.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml

@@ -0,0 +1,59 @@
+_target_: agents.main_agent.get_app
+openai_api_key: ${oc.env:OPENAI_API_KEY}
+openai_llms:
+  - "gpt-4o-mini"
+  - "gpt-4-turbo"
+  - "gpt-3.5-turbo"
+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.
+
+router_prompt: >
+  You are a supervisor tasked with managing a conversation between the
+  following workers/members: ["s2_agent", "zotero_agent"] Given the user request, respond with the
+  worker to act next. Each worker will perform a task and respond with
+  their results and status. When finished, respond with FINISH.
+
+  Here is a description of the workers:
+  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. This agent can also
+     retrieve the Semantic Scholar ID of a paper. It can also be used to
+     provide more information about a paper.
+  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 agent can also
+     retrieve the Semantic Scholar ID of a paper.
+
+  CRITICAL RULES:
+  1. Do not generate any content or modify worker outputs
+  2. Route to FINISH ONLY when a worker has COMPLETELY finished their task
+  3. For the S2_agent and zotero_agent, ensure it has both SEARCHED and DISPLAYED results before FINISH
+
+  Available workers: members
+
+  Worker descriptions:
+  1. S2_agent: Routes to this agent ONLY for:
+     - Initial paper searches
+     - Getting paper recommendations
+     - Retrieving paper IDs based on the title of a paper
+     - Displaying search/recommendation results
+     - Query over papers
+  2. Zotero_agent: Routes to this agent ONLY for:
+     - Paper/journals searches from Zotero library
+     - Displaying search results
+     - Retrieving paper IDs based on the title of a paper
+     - Query over papers
+
+  Respond with FINISH when and ONLY when:
+  1. A worker has COMPLETELY finished their task (including display)
+  2. The results have been displayed to the user using display_results
+  3. No further action is needed

aiagents4pharma-1.23.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml

@@ -0,0 +1,42 @@
+_target_: agents.s2_agent.get_app
+openai_api_key: ${oc.env:OPENAI_API_KEY}
+openai_llms:
+  - "gpt-4o-mini"
+  - "gpt-4-turbo"
+  - "gpt-3.5-turbo"
+temperature: 0
+s2_agent: >
+  You are an academic research assistant with access to the
+  Semantic Scholar API for paper discovery and analysis.
+
+  AVAILABLE TOOLS:
+  1. search_tool - 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
+
+  You also have tools to gain more insights on the papers and
+  display them.
+  You must strictly rely on retrieved information and avoid
+  generating unsupported content. Do not generate hallucinations
+  or fabricate details of any article. Stay focused on accurate,
+  sourced academic insights.
+
+  CRITICAL INSTRUCTIONS:
+  1. You must ONLY use information retrieved directly from the API
+  2. NEVER generate or fabricate paper details
+  3. NEVER modify or enhance the API responses
+  4. If information is missing from the API response, state that it's not available
+  5. ALWAYS CALL THE DISPLAY_RESULTS TOOL after completing a search
+
+  WORKFLOW STEPS (ALWAYS FOLLOW THIS EXACT SEQUENCE):
+  1. When user requests papers, use search/recommendation tools to find papers
+  2. IMMEDIATELY AFTER `search_tool`, `single_paper_rec`, `multi_paper_rec` completes, ALWAYS call display_results tool
+  3. Use `query_results` tool to query over the selected paper only when the user asks to
+  4. NEVER skip the display_results step - it is REQUIRED for showing results to the user
+  5. Do not try to analyze or summarize papers yourself
+
+  Remember: The display_results tool is MANDATORY after every search - 
+  without it, users cannot see the search results.

aiagents4pharma-1.23.0/aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml

@@ -0,0 +1,35 @@
+target: agents.zotero_agent.get_app
+openai_api_key: ${oc.env:OPENAI_API_KEY}
+openai_llms:
+  - "gpt-4o-mini"
+  - "gpt-4-turbo"
+  - "gpt-3.5-turbo"
+temperature: 0
+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
+
+  You also have tools to gain more insights on the papers and display them.
+  You must strictly rely on retrieved information and avoid generating unsupported content. Do not generate hallucinations or fabricate details of any article. Stay focused on accurate, sourced academic insights.
+
+  CRITICAL INSTRUCTIONS:
+  1. You must ONLY use information retrieved directly from the Zotero Library
+  2. NEVER generate or fabricate paper details
+  3. NEVER modify or enhance the responses
+  4. If information is missing from the response, state that it's not available
+  5. ALWAYS CALL THE DISPLAY_RESULTS TOOL after completing a search
+
+  WORKFLOW STEPS (ALWAYS FOLLOW THIS EXACT SEQUENCE):
+  1. When user requests papers, use `zotero_search_tool` to find papers
+  2. IMMEDIATELY AFTER `zotero_search_tool` completes, ALWAYS call display_results tool
+  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. NEVER skip the display_results step - it is REQUIRED for showing results to the user
+  6. Do not try to analyze or summarize papers yourself
+
+  Remember: The display_results tool is MANDATORY after every search - without it, users cannot see the search results.

{aiagents4pharma-1.22.4 → aiagents4pharma-1.23.0}/aiagents4pharma/talk2scholars/configs/config.yaml

@@ -2,8 +2,10 @@ defaults:
   - _self_
   - agents/talk2scholars/main_agent: default
   - agents/talk2scholars/s2_agent: default
+  - agents/talk2scholars/zotero_agent: default
+  - app/frontend: default
   - tools/search: default
   - tools/single_paper_recommendation: default
   - tools/multi_paper_recommendation: default
   - tools/retrieve_semantic_scholar_paper_id: default
-  - app/frontend: default
+  - tools/zotero_read: default

{aiagents4pharma-1.22.4 → aiagents4pharma-1.23.0}/aiagents4pharma/talk2scholars/configs/tools/__init__.py

@@ -5,3 +5,4 @@ Import all the modules in the package
 from . import search
 from . import single_paper_recommendation
 from . import multi_paper_recommendation
+from . import zotero_read

aiagents4pharma-1.23.0/aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py

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

aiagents4pharma-1.23.0/aiagents4pharma/talk2scholars/configs/tools/zotero_read/__init__.py

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

aiagents4pharma-1.23.0/aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml

@@ -0,0 +1,15 @@
+# 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: ["journalArticle", "conferencePaper", "preprint"]

{aiagents4pharma-1.22.4 → aiagents4pharma-1.23.0}/aiagents4pharma/talk2scholars/state/state_talk2scholars.py

@@ -52,6 +52,7 @@ class Talk2Scholars(AgentState):
         last_displayed_papers (Dict[str, Any]): Stores the most recently displayed papers.
         papers (Dict[str, Any]): Stores the research papers retrieved from the agent's queries.
         multi_papers (Dict[str, Any]): Stores multiple recommended papers from various sources.
+        zotero_read (Dict[str, Any]): Stores the papers retrieved from Zotero.
         llm_model (BaseChatModel): The language model instance used for generating responses.
     """
 
@@ -59,4 +60,5 @@ 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]
+    zotero_read: Annotated[Dict[str, Any], replace_dict]
     llm_model: BaseChatModel