aiagents4pharma 1.27.2__py3-none-any.whl → 1.29.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python3
+
+"""
+Utility functions for Zotero tools.
+"""
+
+import logging
+
+# Configure logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def get_item_collections(zot):
+    """
+    Fetch all Zotero collections and map item keys to their full collection paths.
+
+    Args:
+        zot (Zotero): An initialized Zotero client.
+
+    Returns:
+        dict: A dictionary mapping item keys to a list of full collection paths.
+    """
+    logger.info("Fetching Zotero collections...")
+
+    # Fetch all collections
+    collections = zot.collections()
+
+    # Create mappings: collection key → name and collection key → parent key
+    collection_map = {col["key"]: col["data"]["name"] for col in collections}
+    parent_map = {
+        col["key"]: col["data"].get("parentCollection") for col in collections
+    }
+
+    # Build full paths for collections
+    def build_collection_path(col_key):
+        path = []
+        while col_key:
+            path.insert(0, collection_map.get(col_key, "Unknown"))
+            col_key = parent_map.get(col_key)
+        return "/" + "/".join(path)  # Convert to "/path/to/collection"
+
+    collection_paths = {key: build_collection_path(key) for key in collection_map}
+
+    # Manually create an item-to-collection mapping with full paths
+    item_to_collections = {}
+
+    for collection in collections:
+        collection_key = collection["key"]
+        collection_items = zot.collection_items(
+            collection_key
+        )  # Fetch items in the collection
+
+        for item in collection_items:
+            item_key = item["data"]["key"]
+            if item_key in item_to_collections:
+                item_to_collections[item_key].append(collection_paths[collection_key])
+            else:
+                item_to_collections[item_key] = [collection_paths[collection_key]]
+
+    logger.info("Successfully mapped items to collection paths.")
+
+    return item_to_collections

aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py

@@ -13,6 +13,11 @@ from langchain_core.tools import tool
 from langchain_core.tools.base import InjectedToolCallId
 from langgraph.types import Command
 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)
@@ -27,7 +32,7 @@ class ZoteroSearchInput(BaseModel):
     )
     only_articles: bool = Field(
         default=True,
-        description="Whether to only search for journal articles/" "conference papers.",
+        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
@@ -35,12 +40,6 @@ class ZoteroSearchInput(BaseModel):
     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,
@@ -59,22 +58,55 @@ def zotero_search_tool(
     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,
-    )
+    # Load hydra configuration
+    with hydra.initialize(version_base=None, config_path="../../configs"):
+        cfg = hydra.compose(
+            config_name="config", overrides=["tools/zotero_read=default"]
+        )
+        logger.info("Loaded configuration for Zotero search tool")
+        cfg = cfg.tools.zotero_read
+        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))
+    # Fetch collection mapping once
+    item_to_collections = get_item_collections(zot)
+
+    # If the query is empty, fetch all items (up to max_limit), otherwise use the query
+    try:
+        if query.strip() == "":
+            logger.info(
+                "Empty query provided, fetching all items up to max_limit: %d",
+                cfg.zotero.max_limit,
+            )
+            items = zot.items(limit=cfg.zotero.max_limit)
+        else:
+            items = zot.items(q=query, limit=min(limit, cfg.zotero.max_limit))
+    except Exception as e:
+        logger.error("Failed to fetch items from Zotero: %s", e)
+        raise RuntimeError(
+            "Failed to fetch items from Zotero. Please retry the same query."
+        ) from e
+
     logger.info("Received %d items from Zotero", len(items))
 
+    if not items:
+        logger.error("No items returned from Zotero for query: '%s'", query)
+        raise RuntimeError(
+            "No items returned from Zotero. Please retry the same query."
+        )
+
     # Define filter criteria
     filter_item_types = cfg.zotero.filter_item_types if only_articles else []
+    filter_excluded_types = (
+        cfg.zotero.filter_excluded_types
+    )  # Exclude non-research items
 
     # Filter and format papers
     filtered_papers = {}
@@ -88,10 +120,16 @@ def zotero_search_tool(
             continue
 
         item_type = data.get("itemType")
-        if only_articles and (
+        logger.debug("Item type: %s", item_type)
+
+        # Exclude attachments, notes, and other unwanted types
+        if (
             not item_type
             or not isinstance(item_type, str)
-            or item_type not in filter_item_types
+            or item_type in filter_excluded_types  # Skip attachments & notes
+            or (
+                only_articles and item_type not in filter_item_types
+            )  # Skip non-research types
         ):
             continue
 
@@ -99,20 +137,27 @@ def zotero_search_tool(
         if not key:
             continue
 
+        # Use the imported utility function's mapping to get collection paths
+        collection_paths = item_to_collections.get(key, ["/Unknown"])
+
         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",
+            "Collections": collection_paths,  # Now displays full paths
         }
 
     if not filtered_papers:
-        logger.warning("No matching papers found for query: '%s'", query)
+        logger.error("No matching papers returned from Zotero for query: '%s'", query)
+        raise RuntimeError(
+            "No matching papers returned from Zotero. Please retry the same query."
+        )
 
     logger.info("Filtered %d items", len(filtered_papers))
 
-    # Prepare content with top 3 paper titles and types
+    # Prepare content with top 2 paper titles and types
     top_papers = list(filtered_papers.values())[:2]
     top_papers_info = "\n".join(
         [

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-1.27.2.dist-info → aiagents4pharma-1.29.0.dist-info}/METADATA

@@ -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.dist-info → aiagents4pharma-1.29.0.dist-info}/RECORD

@@ -135,59 +135,75 @@ 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=WxEauzCzLEGyhdIRkxSBpNW5c_Uzf7iJUdM57IQkXH8,144
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=nZIhOyEUSHECM4-wEHbDrfHRLkqoxW0H4fy6-MpA6N8,9397
-aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=ZiXtQVX2UbIyMOSXajuloWepEm7DKs6ZpPS0HgHzw0g,4492
-aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=flIvg1ORaMiQpGEbsRM4zJHRNXi6UUv7emHDjH5HVY4,3961
+aiagents4pharma/talk2scholars/agents/__init__.py,sha256=ZwFiHOlDGJk1601J5xEZDy0btPzqiOk2UCocKxohde8,168
+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=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=IBrHX_mACNb7R4rrI_zbWgscAMUdIAkOg9LDgLN1o28,386
+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=MI4RmoQQ2P-JQgCJ8XEucqF6g2VlNNi37yxcsXFj9Oo,122
+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
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 aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=JoSZV6N669kGMv5zLDszwf0ZjcRHx9TJfIqGhIIdPXE,70
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