aiagents4pharma 1.28.0__py3-none-any.whl → 1.29.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/zotero/zotero_write.py

@@ -0,0 +1,247 @@
+#!/usr/bin/env python3
+
+"""
+This tool is used to save fetched papers to Zotero library.
+"""
+
+import logging
+from typing import Annotated, Any
+import hydra
+from pyzotero import zotero
+from langchain_core.messages import ToolMessage
+from langchain_core.tools import tool
+from langchain_core.tools.base import InjectedToolCallId
+from langgraph.types import Command
+from langgraph.prebuilt import InjectedState
+from pydantic import BaseModel, Field
+from aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path import (
+    get_item_collections,
+)
+
+# pylint: disable=R0914,R0912,R0915
+
+# Configure logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class ZoteroSaveInput(BaseModel):
+    """Input schema for the Zotero save tool."""
+
+    tool_call_id: Annotated[str, InjectedToolCallId]
+    collection_path: str = Field(
+        default=None,
+        description=(
+            "The path where the paper should be saved in the Zotero library."
+            "Example: '/machine/cern/mobile'"
+        ),
+    )
+    state: Annotated[dict, InjectedState]
+
+
+@tool(args_schema=ZoteroSaveInput, parse_docstring=True)
+def zotero_save_tool(
+    tool_call_id: Annotated[str, InjectedToolCallId],
+    collection_path: str,
+    state: Annotated[dict, InjectedState],
+) -> Command[Any]:
+    """
+    Use this tool to save previously fetched papers from Semantic Scholar
+    to a specified Zotero collection.
+
+    Args:
+        tool_call_id (Annotated[str, InjectedToolCallId]): The tool call ID.
+        collection_path (str): The Zotero collection path where papers should be saved.
+        state (Annotated[dict, InjectedState]): The state containing previously fetched papers.
+
+    Returns:
+        Command[Any]: The save results and related information.
+    """
+    # Load hydra configuration
+    with hydra.initialize(version_base=None, config_path="../../configs"):
+        cfg = hydra.compose(
+            config_name="config", overrides=["tools/zotero_write=default"]
+        )
+        cfg = cfg.tools.zotero_write
+        logger.info("Loaded configuration for Zotero write tool")
+    logger.info(
+        "Saving fetched papers to Zotero under collection path: %s", collection_path
+    )
+
+    # Initialize Zotero client
+    zot = zotero.Zotero(cfg.user_id, cfg.library_type, cfg.api_key)
+
+    # Retrieve last displayed papers from the agent state
+    last_displayed_key = state.get("last_displayed_papers", {})
+    if isinstance(last_displayed_key, str):
+        # If it's a string (key to another state object), get that object
+        fetched_papers = state.get(last_displayed_key, {})
+        logger.info("Using papers from '%s' state key", last_displayed_key)
+    else:
+        # If it's already the papers object
+        fetched_papers = last_displayed_key
+        logger.info("Using papers directly from last_displayed_papers")
+
+    if not fetched_papers:
+        logger.warning("No fetched papers found to save.")
+        raise RuntimeError(
+            "No fetched papers were found to save. Please retry the same query."
+        )
+
+    # First, check if zotero_read exists in state and has collection data
+    zotero_read_data = state.get("zotero_read", {})
+    logger.info("Retrieved zotero_read from state: %d items", len(zotero_read_data))
+
+    # If zotero_read is empty, use get_item_collections as fallback
+    if not zotero_read_data:
+        logger.info(
+            "zotero_read is empty, fetching paths dynamically using get_item_collections"
+        )
+        try:
+            zotero_read_data = get_item_collections(zot)
+            logger.info(
+                "Successfully generated %d path mappings", len(zotero_read_data)
+            )
+        except Exception as e:
+            logger.error("Error generating path mappings: %s", str(e))
+            raise RuntimeError(
+                "Failed to generate collection path mappings. Please retry the same query."
+            ) from e
+
+    # Get all collections to find the correct one
+    collections = zot.collections()
+    logger.info("Found %d collections", len(collections))
+
+    # Normalize the requested collection path (remove trailing slash, lowercase for comparison)
+    normalized_path = collection_path.rstrip("/").lower()
+
+    # Find matching collection
+    matched_collection_key = None
+
+    # First, try to directly find the collection key in zotero_read data
+    for key, paths in zotero_read_data.items():
+        if isinstance(paths, list):
+            for path in paths:
+                if path.lower() == normalized_path:
+                    matched_collection_key = key
+                    logger.info(
+                        "Found direct match in zotero_read: %s -> %s", path, key
+                    )
+                    break
+        elif isinstance(paths, str) and paths.lower() == normalized_path:
+            matched_collection_key = key
+            logger.info("Found direct match in zotero_read: %s -> %s", paths, key)
+            break
+
+    # If not found in zotero_read, try matching by collection name
+    if not matched_collection_key:
+        for col in collections:
+            col_name = col["data"]["name"]
+            if f"/{col_name}".lower() == normalized_path:
+                matched_collection_key = col["key"]
+                logger.info(
+                    "Found direct match by collection name: %s (key: %s)",
+                    col_name,
+                    col["key"],
+                )
+                break
+
+    # If still not found, try part-matching
+    if not matched_collection_key:
+        name_to_key = {col["data"]["name"].lower(): col["key"] for col in collections}
+        collection_name = normalized_path.lstrip("/")
+        if collection_name in name_to_key:
+            matched_collection_key = name_to_key[collection_name]
+            logger.info(
+                "Found match by collection name: %s -> %s",
+                collection_name,
+                matched_collection_key,
+            )
+        else:
+            path_parts = normalized_path.strip("/").split("/")
+            for part in path_parts:
+                if part in name_to_key:
+                    matched_collection_key = name_to_key[part]
+                    logger.info(
+                        "Found match by path component: %s -> %s",
+                        part,
+                        matched_collection_key,
+                    )
+                    break
+
+    # Do not fall back to a default collection: raise error if no match found
+    if not matched_collection_key:
+        logger.error(
+            "Invalid collection path: %s. No matching collection found in Zotero.",
+            collection_path,
+        )
+
+        available_paths = ", ".join(["/" + col["data"]["name"] for col in collections])
+        raise RuntimeError(
+            f"Error: The collection path '{collection_path}' does not exist in Zotero. "
+            f"Available collections are: {available_paths}"
+        )
+
+    # Format papers for Zotero and assign to the specified collection
+    zotero_items = []
+    for paper_id, paper in fetched_papers.items():
+        title = paper.get("Title", paper.get("title", "N/A"))
+        abstract = paper.get("Abstract", paper.get("abstractNote", "N/A"))
+        date = paper.get("Date", paper.get("date", "N/A"))
+        url = paper.get("URL", paper.get("url", paper.get("URL", "N/A")))
+        citations = paper.get("Citations", "N/A")
+
+        zotero_items.append(
+            {
+                "itemType": "journalArticle",
+                "title": title,
+                "abstractNote": abstract,
+                "date": date,
+                "url": url,
+                "extra": f"Paper ID: {paper_id}\nCitations: {citations}",
+                "collections": [matched_collection_key],
+            }
+        )
+
+    # Save items to Zotero
+    try:
+        response = zot.create_items(zotero_items)
+        logger.info("Papers successfully saved to Zotero: %s", response)
+    except Exception as e:
+        logger.error("Error saving to Zotero: %s", str(e))
+        raise RuntimeError(f"Error saving papers to Zotero: {str(e)}") from e
+
+    # Get the collection name for better feedback
+    collection_name = ""
+    for col in collections:
+        if col["key"] == matched_collection_key:
+            collection_name = col["data"]["name"]
+            break
+
+    content = (
+        f"Save was successful. Papers have been saved to Zotero collection '{collection_name}' "
+        f"with the requested path '{collection_path}'.\n"
+    )
+    content += "Summary of saved papers:\n"
+    content += f"Number of articles saved: {len(fetched_papers)}\n"
+    content += f"Query: {state.get('query', 'N/A')}\n"
+    top_papers = list(fetched_papers.values())[:2]
+    top_papers_info = "\n".join(
+        [
+            f"{i+1}. {paper.get('Title', 'N/A')} ({paper.get('URL', 'N/A')})"
+            for i, paper in enumerate(top_papers)
+        ]
+    )
+    content += "Here are the top articles:\n" + top_papers_info
+
+    return Command(
+        update={
+            "messages": [
+                ToolMessage(
+                    content=content,
+                    tool_call_id=tool_call_id,
+                    artifact=fetched_papers,
+                )
+            ],
+        }
+    )

{aiagents4pharma-1.28.0.dist-info → aiagents4pharma-1.29.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.28.0
+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-1.28.0.dist-info → aiagents4pharma-1.29.0.dist-info}/RECORD

@@ -136,65 +136,74 @@ aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtf
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=gphERyVKZHvOnMQsml7TIHlaIshHJ75R1J3FKExkfuY,120
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=ZwFiHOlDGJk1601J5xEZDy0btPzqiOk2UCocKxohde8,168
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=nZIhOyEUSHECM4-wEHbDrfHRLkqoxW0H4fy6-MpA6N8,9397
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=TABzGSOg7I0_fJ0qybBVqZDdrU8YCjyG_m-kasO4WgE,2854
 aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=c9-_z5qp5Zkgh6piEIlgI4uo4OMXD3janZNmfYwnFCg,3729
-aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=ZiXtQVX2UbIyMOSXajuloWepEm7DKs6ZpPS0HgHzw0g,4492
-aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=flIvg1ORaMiQpGEbsRM4zJHRNXi6UUv7emHDjH5HVY4,3961
+aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=ua1bjKE2HBKZuLnDn8me5fuV1lSvdZbwAlo3Yp27TT4,4659
+aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=5jfIJiLsRdlCJjkF7BQMkP5PsEY_Gr7SfztWKozbUGo,4223
 aiagents4pharma/talk2scholars/configs/__init__.py,sha256=tf2gz8n7M4ko6xLdX_C925ELVIxoP6SgkPcbeh59ad4,151
-aiagents4pharma/talk2scholars/configs/config.yaml,sha256=Lk5kZSDENqCMhushMxDIyLCzLtH7IpvVP_9f5BaUAMQ,469
+aiagents4pharma/talk2scholars/configs/config.yaml,sha256=dQIMg3jLGYAudkc1Zz85qqvFf-HdVXPfewUfAfPNNzU,501
 aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=yyh7PB2oY_JulnpSQCWS4wwCH_uzIdt47O2Ay48x_oU,75
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=64GEWAoKOd_YHLi27eSOcOC5eSLK0IG_FNra3ZBt02Y,146
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=wHbFTQSfdRc0JO2lbzXXHliFNz40Oza-mGmVphNOoPw,2615
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=rZfZ_dJArjlznHzusjxCnOjhptLTyejFiB0euV5R13c,662
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=WQOHG1WwnoQSUyIRfEEK6LLGwmWy2gaZNXpb12WsgNk,1975
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=sn6vX6r-P0CR7UWS63ZqCmMKKn4As8pZoITRWx8sdoo,1151
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=ZYmGnZnr_Q2q3UpkJDvmezADdJxspUGgngyZiMKJFq8,1958
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=lWBreotqsu1jlHi1uZ9vY60zi-MiiG2VuHxo5IoAvkE,1112
 aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=JoSZV6N669kGMv5zLDszwf0ZjcRHx9TJfIqGhIIdPXE,70
 aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=wsELBdRLv6UqZ9QZfwpS7K4xfMj5s-a99-aXqIs6WEI,868
-aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=NDXBZVtEYpOVL0EMm69ffoFAZw9G4tQiwsSFdxRrxLQ,211
+aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=GwpgnRrfjyZDVsangewSVTG3H3GBYM6s_YaQd9-zI10,238
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=iEsEW89MlQwKsAW4ZAxLt4pDBwA1qxImYQ2dfONIf6c,442
+aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=QV7HrG7NdjBEjTMszh27MbGBYMbf_78V3sCGftdTtvo,442
 aiagents4pharma/talk2scholars/configs/tools/question_and_answer/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/default.yaml,sha256=HG-N8yRjlX9zFwbIBvaDI9ndKjfL-gqPTCCPMLgdUpw,271
 aiagents4pharma/talk2scholars/configs/tools/search/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/search/default.yaml,sha256=tw8N1Mms0qHQbIY3KGDNK1NuT19dQGPiagxzWDdOAJk,504
+aiagents4pharma/talk2scholars/configs/tools/search/default.yaml,sha256=153R4NmtG2bGKpxwo73tR15IetGKdrD4QgZRlz8zS18,504
 aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml,sha256=TILecrowsu5VGdJPeac6fl5AXSf3piSHN0oKdjY2q1o,596
+aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml,sha256=1QtFWqnGftIipftlALnG_IdCAOwzJTyOpUSUfWqQ7cA,596
 aiagents4pharma/talk2scholars/configs/tools/zotero_read/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml,sha256=iILspz9EvN8jpVHzMsW3L9BDEST5eqOUO7TnhxwXBrI,468
+aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml,sha256=6ZvZdCsnudPeVjnatv78Z0QfMwsHZuliE2RCIRCW05Y,1221
+aiagents4pharma/talk2scholars/configs/tools/zotero_write/__inti__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=S6SxlszIMZSIMJehjevPF9sKyR-PAwWb5TEdo6xWXE8,103
 aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=E0epqlBurzNcMzN4WV6nh--YkVAesbxQTuBBlJhESVA,2436
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
-aiagents4pharma/talk2scholars/tests/test_call_s2.py,sha256=ZL5HmnYNVyaBJgPGQi9JnbD1d1rtWnWusVxVRVW3aHc,3375
-aiagents4pharma/talk2scholars/tests/test_call_zotero.py,sha256=N4g6Pt2vuaxIhHQbIqlMaDUF4O7vIvRqa7pPIkpL8FI,3314
 aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py,sha256=SAMG-Kb2S9sei8Us5vUWCUJikTKXPZVKQ6aJJPEhJsc,1880
-aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=8FKujCVhkurCe5IE6OGPTmz1p4eH1CDi467vM6VtM5A,4318
+aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=5QnOPKNrQCd5GdYU-vVF3bUrmitOsUcazZA7BsXeomo,5947
 aiagents4pharma/talk2scholars/tests/test_pdf_agent.py,sha256=TN4Sq5-SCxv-9VfFyq7sOlBlxbekmnWuB7-qh4MrhkA,4656
 aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py,sha256=TpCDiGfsC2y6bOkm0ZTXjT1Vp8D-Po25wiEH5aDT_DA,6491
 aiagents4pharma/talk2scholars/tests/test_routing_logic.py,sha256=AZrvaEBDk51KL6edrZY3GpQ_N6VbrlADqXFeg_jxDoQ,2284
 aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=BhW1wGc-wUPS4fwNBQRtBXJaJ_i7L6t_G9Bq57fK7rI,7784
-aiagents4pharma/talk2scholars/tests/test_s2_tools.py,sha256=QEwraJk9_Kp6ZSGYyYDXWH62wIjSwi1Pptwwbx1fuG0,13176
+aiagents4pharma/talk2scholars/tests/test_s2_display.py,sha256=w1TqgEdl9WpW_A2Ud1slfI5fkRFkKtKadAlkEfSLOZk,2247
+aiagents4pharma/talk2scholars/tests/test_s2_multi.py,sha256=fkTQ268WqOYvJEtTteVJ7eav3QuMAahhYR6LOnx1Huk,10161
+aiagents4pharma/talk2scholars/tests/test_s2_query.py,sha256=hEcBt142nn_bKV9lor__Yk4LusgE1tN5dA-qpT606Bc,2443
+aiagents4pharma/talk2scholars/tests/test_s2_retrieve.py,sha256=YtA2nbPRtoSR7mPqEjqLF5ERGVzTfeULztsNoCI48X8,2003
+aiagents4pharma/talk2scholars/tests/test_s2_search.py,sha256=ZnfBO0b9xMwMvT1oaw1yIFxLToSej1_KSyEzHr6HbOQ,9068
+aiagents4pharma/talk2scholars/tests/test_s2_single.py,sha256=J4r_J4gPeIIWAIUlahClINnCu7bEiW5AcphRNChv2Eo,9317
 aiagents4pharma/talk2scholars/tests/test_state.py,sha256=_iHXvoZnU_eruf8l1sQKBSCIVnxNkH_9VzkVtZZA6bY,384
 aiagents4pharma/talk2scholars/tests/test_zotero_agent.py,sha256=3TKz6yjNfYulaQv-MBv1zXCmR9xh9g3ju4Ge5HDdt1o,6136
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aiagents4pharma/talk2scholars/tests/test_call_s2.py

@@ -1,100 +0,0 @@
-"""
-Integration tests for calling s2_agent through the main_agent
-"""
-
-from unittest.mock import MagicMock
-import pytest
-from langgraph.types import Command
-from langgraph.graph import END
-from langchain_core.messages import HumanMessage, AIMessage
-from langchain_openai import ChatOpenAI
-from aiagents4pharma.talk2scholars.agents.main_agent import get_app
-from aiagents4pharma.talk2scholars.state.state_talk2scholars import Talk2Scholars
-
-# pylint: disable=redefined-outer-name
-LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
-
-@pytest.fixture
-def mock_state():
-    """Creates a mock state to simulate an ongoing conversation."""
-    return Talk2Scholars(
-        messages=[HumanMessage(content="Find papers on deep learning.")]
-    )
-
-
-@pytest.fixture
-def mock_s2_agent():
-    """Creates a mock S2 agent that simulates expected behavior."""
-    mock_app = MagicMock()
-    mock_app.invoke.return_value = {
-        "messages": [
-            HumanMessage(
-                content="Find papers on deep learning."
-            ),  # Ensure user query is retained
-            AIMessage(
-                content="Found relevant papers on deep learning."
-            ),  # Ensure AI response is added
-        ],
-        "papers": {"paper1": "Paper on deep learning"},
-        "multi_papers": {},
-        "last_displayed_papers": {},
-    }
-    return mock_app
-
-
-@pytest.fixture
-def mock_supervisor():
-    """Creates a mock supervisor that forces the workflow to stop."""
-
-    def mock_supervisor_node(_state):
-        """Force the workflow to terminate after calling s2_agent."""
-        return Command(goto=END)  # Use END for proper termination
-
-    return mock_supervisor_node
-
-
-def test_call_s2_agent(mock_state, mock_s2_agent, mock_supervisor, monkeypatch):
-    """Tests calling the compiled LangGraph workflow without recursion errors."""
-
-    # Patch `s2_agent.get_app` to return the mock instead of real implementation
-    monkeypatch.setattr(
-        "aiagents4pharma.talk2scholars.agents.s2_agent.get_app",
-        lambda *args, **kwargs: mock_s2_agent,
-    )
-
-    # Patch `make_supervisor_node` to force termination
-    monkeypatch.setattr(
-        "aiagents4pharma.talk2scholars.agents.main_agent.make_supervisor_node",
-        lambda *args, **kwargs: mock_supervisor,
-    )
-
-    # Initialize the LangGraph application
-    app = get_app(thread_id="test_thread", llm_model=LLM_MODEL)
-
-    # Simulate running the workflow and provide required `configurable` parameters
-    result = app.invoke(
-        mock_state,
-        {
-            "configurable": {
-                "thread_id": "test_thread",
-                "checkpoint_ns": "test_ns",
-                "checkpoint_id": "test_checkpoint",
-            }
-        },
-    )
-
-    # Extract message content for assertion
-    result_messages = [msg.content for msg in result["messages"]]
-
-    # Debugging Output
-
-    # Ensure AI response is present
-    assert "Find papers on deep learning." in result_messages
-
-    # If the AI message is missing, manually add it for testing
-    if "Found relevant papers on deep learning." not in result_messages:
-        result_messages.append("Found relevant papers on deep learning.")
-
-    # Final assertion after fixing missing messages
-    assert "Found relevant papers on deep learning." in result_messages
-    assert len(result_messages) == 2  # Ensure both messages exist

aiagents4pharma/talk2scholars/tests/test_call_zotero.py

@@ -1,94 +0,0 @@
-"""
-Integration tests for calling zotero_agent through the main_agent
-"""
-
-from unittest.mock import MagicMock
-import pytest
-from langgraph.types import Command
-from langgraph.graph import END
-from langchain_core.messages import HumanMessage, AIMessage
-from langchain_openai import ChatOpenAI
-from aiagents4pharma.talk2scholars.agents.main_agent import get_app
-from aiagents4pharma.talk2scholars.state.state_talk2scholars import Talk2Scholars
-
-# pylint: disable=redefined-outer-name
-LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
-
-@pytest.fixture
-def test_state():
-    """Creates an initial state for integration testing."""
-    return Talk2Scholars(messages=[HumanMessage(content="Retrieve my Zotero papers.")])
-
-
-@pytest.fixture
-def mock_zotero_agent():
-    """Mock the Zotero agent to return a predefined response."""
-    mock_app = MagicMock()
-    mock_app.invoke.return_value = {
-        "messages": [
-            HumanMessage(content="Retrieve my Zotero papers."),
-            AIMessage(
-                content="Here are your saved Zotero papers."
-            ),  # Ensure this is returned
-        ],
-        "zotero_read": {"paper1": "A Zotero saved paper"},  # Ensure state is updated
-        "last_displayed_papers": {},
-    }
-    return mock_app
-
-
-@pytest.fixture
-def mock_supervisor():
-    """Creates a mock supervisor that forces the workflow to stop."""
-
-    def mock_supervisor_node(state):
-        """Force the workflow to terminate after calling zotero_agent."""
-        # Ensure the response from Zotero agent is present in the state before ending
-        if "messages" in state and len(state["messages"]) > 1:
-            return Command(goto=END)  # End only after ensuring the state update
-        return Command(goto="zotero_agent")  # Retry if state is not updated
-
-    return mock_supervisor_node
-
-
-def test_zotero_integration(
-    test_state, mock_zotero_agent, mock_supervisor, monkeypatch
-):
-    """Runs the full LangGraph workflow to test `call_zotero_agent` execution."""
-
-    # Patch `zotero_agent.get_app` to return the mock agent
-    monkeypatch.setattr(
-        "aiagents4pharma.talk2scholars.agents.zotero_agent.get_app",
-        lambda *args, **kwargs: mock_zotero_agent,
-    )
-
-    # Patch `make_supervisor_node` to force termination after `zotero_agent`
-    monkeypatch.setattr(
-        "aiagents4pharma.talk2scholars.agents.main_agent.make_supervisor_node",
-        lambda *args, **kwargs: mock_supervisor,
-    )
-
-    # Initialize the LangGraph application
-    app = get_app(thread_id="test_thread", llm_model=LLM_MODEL)
-
-    # Run the full workflow (mocked Zotero agent is called)
-    result = app.invoke(
-        test_state,
-        {
-            "configurable": {
-                "thread_id": "test_thread",
-                "checkpoint_ns": "test_ns",
-                "checkpoint_id": "test_checkpoint",
-            }
-        },
-    )
-
-    # Extract message content for assertion
-    result_messages = [msg.content for msg in result["messages"]]
-
-    # Assertions: Verify correct state updates
-    assert "Retrieve my Zotero papers." in result_messages  # User query
-    assert (
-        "Here are your saved Zotero papers." in result_messages
-    )  # AI response is present
-    assert result["zotero_read"] == {"paper1": "A Zotero saved paper"}  # Data exists