aiagents4pharma 1.22.4__py3-none-any.whl → 1.23.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python3
+
+"""
+This tool is used to search for papers in 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 pydantic import BaseModel, Field
+
+# Configure logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class ZoteroSearchInput(BaseModel):
+    """Input schema for the Zotero search tool."""
+
+    query: str = Field(
+        description="Search query string to find papers in Zotero library."
+    )
+    only_articles: bool = Field(
+        default=True,
+        description="Whether to only search for journal articles/" "conference papers.",
+    )
+    limit: int = Field(
+        default=2, description="Maximum number of results to return", ge=1, le=100
+    )
+    tool_call_id: Annotated[str, InjectedToolCallId]
+
+
+# Load hydra configuration
+with hydra.initialize(version_base=None, config_path="../../configs"):
+    cfg = hydra.compose(config_name="config", overrides=["tools/zotero_read=default"])
+    cfg = cfg.tools.zotero_read
+
+
+@tool(args_schema=ZoteroSearchInput, parse_docstring=True)
+def zotero_search_tool(
+    query: str,
+    only_articles: bool,
+    tool_call_id: Annotated[str, InjectedToolCallId],
+    limit: int = 2,
+) -> Command[Any]:
+    """
+    Use this tool to search and retrieve papers from Zotero library.
+
+    Args:
+        query (str): The search query string to find papers.
+        tool_call_id (Annotated[str, InjectedToolCallId]): The tool call ID.
+        limit (int, optional): The maximum number of results to return. Defaults to 2.
+
+    Returns:
+        Dict[str, Any]: The search results and related information.
+    """
+    logger.info(
+        "Searching Zotero for query: '%s' (only_articles: %s, limit: %d)",
+        query,
+        only_articles,
+        limit,
+    )
+
+    # Initialize Zotero client
+    zot = zotero.Zotero(cfg.user_id, cfg.library_type, cfg.api_key)
+
+    # Get items matching the query
+    items = zot.items(q=query, limit=min(limit, cfg.zotero.max_limit))
+    logger.info("Received %d items from Zotero", len(items))
+
+    # Define filter criteria
+    filter_item_types = cfg.zotero.filter_item_types if only_articles else []
+
+    # Filter and format papers
+    filtered_papers = {}
+
+    for item in items:
+        if not isinstance(item, dict):
+            continue
+
+        data = item.get("data")
+        if not isinstance(data, dict):
+            continue
+
+        item_type = data.get("itemType")
+        if only_articles and (
+            not item_type
+            or not isinstance(item_type, str)
+            or item_type not in filter_item_types
+        ):
+            continue
+
+        key = data.get("key")
+        if not key:
+            continue
+
+        filtered_papers[key] = {
+            "Title": data.get("title", "N/A"),
+            "Abstract": data.get("abstractNote", "N/A"),
+            "Date": data.get("date", "N/A"),
+            "URL": data.get("url", "N/A"),
+            "Type": item_type if isinstance(item_type, str) else "N/A",
+        }
+
+    if not filtered_papers:
+        logger.warning("No matching papers found for query: '%s'", query)
+
+    logger.info("Filtered %d items", len(filtered_papers))
+
+    # Prepare content with top 3 paper titles and types
+    top_papers = list(filtered_papers.values())[:2]
+    top_papers_info = "\n".join(
+        [
+            f"{i+1}. {paper['Title']} ({paper['Type']})"
+            for i, paper in enumerate(top_papers)
+        ]
+    )
+
+    content = "Retrieval was successful. Papers are attached as an artifact."
+    content += " And here is a summary of the retrieval results:\n"
+    content += f"Number of papers found: {len(filtered_papers)}\n"
+    content += f"Query: {query}\n"
+    content += "Top papers:\n" + top_papers_info
+
+    return Command(
+        update={
+            "zotero_read": filtered_papers,
+            "last_displayed_papers": "zotero_read",
+            "messages": [
+                ToolMessage(
+                    content=content,
+                    tool_call_id=tool_call_id,
+                    artifact=filtered_papers,
+                )
+            ],
+        }
+    )

{aiagents4pharma-1.22.4.dist-info → aiagents4pharma-1.23.0.dist-info}/METADATA

@@ -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.dist-info → aiagents4pharma-1.23.0.dist-info}/RECORD

@@ -124,21 +124,24 @@ aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py,sha256
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtfzKhB8GuOBD47XRi0NprwEXkOzwNl5eeu-hDTI,86
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=gphERyVKZHvOnMQsml7TIHlaIshHJ75R1J3FKExkfuY,120
-aiagents4pharma/talk2scholars/agents/__init__.py,sha256=ykszlVGxz3egLHZAttlNoTPxIrnQJZYva_ssR8fwIFk,117
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=UiiqCMUko4t39uR4NtTvG3kRMf89x67dU_3NSAM4DWw,7603
+aiagents4pharma/talk2scholars/agents/__init__.py,sha256=WxEauzCzLEGyhdIRkxSBpNW5c_Uzf7iJUdM57IQkXH8,144
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=ZJf1VAk2eA4Hxk8L7K2btiHTrv1CWRxebf4PAJbntuE,9487
 aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=XilKQvlxEVNYK5cEc44x-62OZZ1qG77v1r0FkwLexcw,4581
+aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=E-w4avjDLviwrNOII0gVtHYLeO4wv2umykICJLZxfMU,4049
 aiagents4pharma/talk2scholars/configs/__init__.py,sha256=tf2gz8n7M4ko6xLdX_C925ELVIxoP6SgkPcbeh59ad4,151
-aiagents4pharma/talk2scholars/configs/config.yaml,sha256=XaUi1aP0VGiZFeW_ZP68bVSiCJezied5yLzcx3Uljhc,308
+aiagents4pharma/talk2scholars/configs/config.yaml,sha256=IBrHX_mACNb7R4rrI_zbWgscAMUdIAkOg9LDgLN1o28,386
 aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=yyh7PB2oY_JulnpSQCWS4wwCH_uzIdt47O2Ay48x_oU,75
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=Tj4urOkjpu2cTlpJl0Fmr_18RZCR88vns-Gt-XquDzs,95
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=MI4RmoQQ2P-JQgCJ8XEucqF6g2VlNNi37yxcsXFj9Oo,122
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=kizyUjDasjv3zt2xHcGMqTxnpR_FHAcOs1vgVaH7tsY,1882
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=wHbFTQSfdRc0JO2lbzXXHliFNz40Oza-mGmVphNOoPw,2615
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=lQUvQDLqqPIxn4TkL58atG2dQFhysNuNyAbd6P8km3g,585
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=WQOHG1WwnoQSUyIRfEEK6LLGwmWy2gaZNXpb12WsgNk,1975
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
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 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=w0BJK0MR6Et8Pw1htP8JV0Lr9F_N68CqvbpV14KBy_8,151
+aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=z5PzYS1WyoC4PiWVIIOGICldps2yMh2E_2HFZA9ltpQ,177
 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/retrieve_semantic_scholar_paper_id/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
@@ -147,24 +150,33 @@ aiagents4pharma/talk2scholars/configs/tools/search/__init__.py,sha256=fqQQ-GlRcb
 aiagents4pharma/talk2scholars/configs/tools/search/default.yaml,sha256=tw8N1Mms0qHQbIY3KGDNK1NuT19dQGPiagxzWDdOAJk,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/zotero_read/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml,sha256=iILspz9EvN8jpVHzMsW3L9BDEST5eqOUO7TnhxwXBrI,468
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=S6SxlszIMZSIMJehjevPF9sKyR-PAwWb5TEdo6xWXE8,103
-aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=Jbwckhhpv03KFQYkYkuPsYz5OxT0Si-mra7qrynH5Jo,2246
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 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
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 aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py,sha256=SAMG-Kb2S9sei8Us5vUWCUJikTKXPZVKQ6aJJPEhJsc,1880
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 aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=-yEoG2v5SMkCLCrSA2DFcNE-xMOSn97N4UTomzCeW40,7559
 aiagents4pharma/talk2scholars/tests/test_s2_tools.py,sha256=QEwraJk9_Kp6ZSGYyYDXWH62wIjSwi1Pptwwbx1fuG0,13176
 aiagents4pharma/talk2scholars/tests/test_state.py,sha256=_iHXvoZnU_eruf8l1sQKBSCIVnxNkH_9VzkVtZZA6bY,384
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 aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=wytqCmGm8Fbl8y5qLdIkxhhG8VHLYMifCGjbH_LK2Fc,258
 aiagents4pharma/talk2scholars/tools/s2/display_results.py,sha256=UR0PtEHGDpOhPH0Di5HT8-Fip2RkEMTJgzROsChb1gc,2959
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 aiagents4pharma/talk2scholars/tools/s2/query_results.py,sha256=EUfzRh5Qc_tMl5fDIFb9PIsQkkrU4Xb5MR0sud_X5-c,2017
 aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=Lg1L4HQCN2LaQEyWtLD73O67PMoXkPHi-Y8rCzHS0A4,2499
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