aiagents4pharma 1.30.0__py3-none-any.whl → 1.30.2__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/zotero/zotero_write.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 """
-This tool is used to save fetched papers to Zotero library.
+This tool is used to save fetched papers to Zotero library after human approval.
 """
 
 import logging
@@ -14,11 +14,13 @@ 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,
+from .utils.zotero_path import (
+    find_or_create_collection,
+    fetch_papers_for_save,
 )
 
-# pylint: disable=R0914,R0912,R0915
+
+# pylint: disable=R0914,R0911,R0912,R0915
 
 # Configure logging
 logging.basicConfig(level=logging.INFO)
@@ -30,29 +32,31 @@ class ZoteroSaveInput(BaseModel):
 
     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'"
-        ),
+        description="The path where the paper should be saved in the Zotero library."
     )
     state: Annotated[dict, InjectedState]
 
 
 @tool(args_schema=ZoteroSaveInput, parse_docstring=True)
-def zotero_save_tool(
+def zotero_write(
     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.
+    to a specified Zotero collection after human approval.
+
+    This tool checks if the user has approved the save operation via the
+    zotero_review. If approved, it will save the papers to the
+    approved collection path.
 
     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.
+        user_confirmation (str, optional): User confirmation message when interrupt is
+        not available.
 
     Returns:
         Command[Any]: The save results and related information.
@@ -71,135 +75,96 @@ def zotero_save_tool(
     # 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")
+    # Use our utility function to fetch papers from state
+    fetched_papers = fetch_papers_for_save(state)
 
     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"
+        raise ValueError(
+            "No fetched papers were found to save. "
+            "Please retrieve papers using Zotero Read or Semantic Scholar first."
         )
-        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)
+    # Normalize the requested collection path
     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
+    # Use our utility function to find or optionally create the collection
+    # First try to find the exact collection
+    matched_collection_key = find_or_create_collection(
+        zot, normalized_path, create_missing=False  # First try without creating
+    )
 
-    # 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,
+        # Get all collection names without hierarchy for clearer display
+        available_collections = zot.collections()
+        collection_names = [col["data"]["name"] for col in available_collections]
+        names_display = ", ".join(collection_names)
+
+        return Command(
+            update={
+                "messages": [
+                    ToolMessage(
+                        content=(
+                            f"Error: The collection path '{collection_path}' does "
+                            f"not exist in Zotero. "
+                            f"Available collections are: {names_display}. "
+                            f"Please try saving to one of these existing collections."
+                        ),
+                        tool_call_id=tool_call_id,
                     )
-                    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")
+        title = paper.get("Title", "N/A")
+        abstract = paper.get("Abstract", "N/A")
+        publication_date = paper.get("Publication Date", "N/A")  # Use Publication Date
+        url = paper.get("URL", "N/A")
+        citations = paper.get("Citation Count", "N/A")
+        venue = paper.get("Venue", "N/A")
+        publication_venue = paper.get("Publication Venue", "N/A")
+        journal_name = paper.get("Journal Name", "N/A")
+        journal_volume = paper.get("Journal Volume", "N/A")
+        journal_pages = paper.get("Journal Pages", "N/A")
+
+        # Convert Authors list to Zotero format
+        authors = [
+            (
+                {
+                    "creatorType": "author",
+                    "firstName": name.split(" ")[0],
+                    "lastName": " ".join(name.split(" ")[1:]),
+                }
+                if " " in name
+                else {"creatorType": "author", "lastName": name}
+            )
+            for name in [
+                author.split(" (ID: ")[0] for author in paper.get("Authors", [])
+            ]
+        ]
 
         zotero_items.append(
             {
                 "itemType": "journalArticle",
                 "title": title,
                 "abstractNote": abstract,
-                "date": date,
+                "date": publication_date,  # Now saving full publication date
                 "url": url,
                 "extra": f"Paper ID: {paper_id}\nCitations: {citations}",
                 "collections": [matched_collection_key],
+                "publicationTitle": (
+                    publication_venue if publication_venue != "N/A" else venue
+                ),  # Use publication venue if available
+                "journalAbbreviation": journal_name,  # Save Journal Name
+                "volume": (
+                    journal_volume if journal_volume != "N/A" else None
+                ),  # Save Journal Volume
+                "pages": (
+                    journal_pages if journal_pages != "N/A" else None
+                ),  # Save Journal Pages
+                "creators": authors,  # Save authors list properly
             }
         )
 
@@ -212,6 +177,7 @@ def zotero_save_tool(
         raise RuntimeError(f"Error saving papers to Zotero: {str(e)}") from e
 
     # Get the collection name for better feedback
+    collections = zot.collections()
     collection_name = ""
     for col in collections:
         if col["key"] == matched_collection_key:
@@ -232,8 +198,9 @@ def zotero_save_tool(
             for i, paper in enumerate(top_papers)
         ]
     )
-    content += "Here are the top articles:\n" + top_papers_info
+    content += "Here are a few of these articles:\n" + top_papers_info
 
+    # Clear the approval info so it's not reused
     return Command(
         update={
             "messages": [
@@ -243,5 +210,6 @@ def zotero_save_tool(
                     artifact=fetched_papers,
                 )
             ],
+            "zotero_write_approval_status": {},  # Clear approval info
         }
     )

{aiagents4pharma-1.30.0.dist-info → aiagents4pharma-1.30.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.30.0
+Version: 1.30.2
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -23,7 +23,7 @@ Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
 Requires-Dist: langchain-openai==0.2.5
 Requires-Dist: langchain_ollama==0.2.3
-Requires-Dist: langgraph_supervisor==0.0.4
+Requires-Dist: langgraph_supervisor==0.0.9
 Requires-Dist: matplotlib==3.9.2
 Requires-Dist: openai==1.59.4
 Requires-Dist: ollama==0.4.7
@@ -62,6 +62,7 @@ Requires-Dist: umap-learn==0.5.7
 Requires-Dist: plotly-express==0.4.1
 Requires-Dist: seaborn==0.13.2
 Requires-Dist: scanpy==1.11.0
+Dynamic: license-file
 
 [![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
 [![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)

{aiagents4pharma-1.30.0.dist-info → aiagents4pharma-1.30.2.dist-info}/RECORD

@@ -136,83 +136,86 @@ 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=inLJpRDlT80RNSi3OFNi2lpbbTisQgzNkMYTvnhFjVY,203
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=TABzGSOg7I0_fJ0qybBVqZDdrU8YCjyG_m-kasO4WgE,2854
-aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=3GxxNhA_VGf3QOozIjr5cEY2te5n6rQSdZpdFajZttA,3006
-aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=c9-_z5qp5Zkgh6piEIlgI4uo4OMXD3janZNmfYwnFCg,3729
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=KdKbnc-5zxktLUkzEZHC3bvn8_iKa8Kk4So90i48cdE,3275
+aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=wrK9CPy5evH56fyOZ2BlkBfY5aEj6tefc4jSDPVzYvs,3041
+aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=xt_bgCTVJ6jOCkhc_rHh8pngq4uS8kuNOevuP3eC-sA,3702
 aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=ua1bjKE2HBKZuLnDn8me5fuV1lSvdZbwAlo3Yp27TT4,4659
-aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=5jfIJiLsRdlCJjkF7BQMkP5PsEY_Gr7SfztWKozbUGo,4223
+aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=f11kNqtyZnpBiIf3Fe9gU0WqQ0-ohhngTKl-o0u997Q,4442
 aiagents4pharma/talk2scholars/configs/__init__.py,sha256=tf2gz8n7M4ko6xLdX_C925ELVIxoP6SgkPcbeh59ad4,151
 aiagents4pharma/talk2scholars/configs/config.yaml,sha256=-8X0_gTmjEuXAeIrnppw3Npy8HICelHZOvTKEScI-rs,596
 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=rZfZ_dJArjlznHzusjxCnOjhptLTyejFiB0euV5R13c,662
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=GZRqZoUy8eAWXyd9GJDh-A4mYSJOhnkid6TaIJTGBeU,1192
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 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=sn6vX6r-P0CR7UWS63ZqCmMKKn4As8pZoITRWx8sdoo,1151
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=UIYkr060IpoLHMXVPxGAjrkCJSjX7H0DzcFSasyW6sE,1185
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=lWBreotqsu1jlHi1uZ9vY60zi-MiiG2VuHxo5IoAvkE,1112
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=09nMAlI4CTLlss03trR0ZaEeLdABQfkwUUE6ZCK4WzY,718
 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/app/frontend/default.yaml,sha256=A6nYjrgzEyRv5JYsGN7oqNX4-tufMBZ6mg-A7bMX6V4,906
 aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=GwpgnRrfjyZDVsangewSVTG3H3GBYM6s_YaQd9-zI10,238
 aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=QV7HrG7NdjBEjTMszh27MbGBYMbf_78V3sCGftdTtvo,442
+aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=comNgL9hRpH--IWuEsrN6hV5WdrJmh-ZsRh7hbryVhg,631
 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=153R4NmtG2bGKpxwo73tR15IetGKdrD4QgZRlz8zS18,504
+aiagents4pharma/talk2scholars/configs/tools/search/default.yaml,sha256=RlORkZFLDKFXQqjXjTM0NqsHyLDTIfirbWlAAXrAT00,694
 aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml,sha256=1QtFWqnGftIipftlALnG_IdCAOwzJTyOpUSUfWqQ7cA,596
+aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/default.yaml,sha256=PFXz5oRpNbjQp789QlgmyXktdVWwwVfoYi7mAnlRgik,785
 aiagents4pharma/talk2scholars/configs/tools/zotero_read/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml,sha256=6ZvZdCsnudPeVjnatv78Z0QfMwsHZuliE2RCIRCW05Y,1221
+aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml,sha256=ifOtX8Huj1LPHF_rRe1JxWgrDaLiKg6HVoQen_1R1Ls,1223
 aiagents4pharma/talk2scholars/configs/tools/zotero_write/__inti__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/zotero_write/default.yaml,sha256=gB7y7pznviQUzu49Eu4ONNkjQjT8wPKNSw6S_vfd9kI,1222
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=S6SxlszIMZSIMJehjevPF9sKyR-PAwWb5TEdo6xWXE8,103
-aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=0dFSdsGiiilNIuuHQFEjpjQmcZXlK0JQwMV_GCiAsuU,2490
+aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=8ZFfv55tXO3LU-2DzKC5JjH4_ryodgu-H1ieKBmVFvw,2844
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
-aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py,sha256=SAMG-Kb2S9sei8Us5vUWCUJikTKXPZVKQ6aJJPEhJsc,1880
-aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=5QnOPKNrQCd5GdYU-vVF3bUrmitOsUcazZA7BsXeomo,5947
+aiagents4pharma/talk2scholars/tests/test_llm_main_integration.py,sha256=FBRqS06IKJYFOudQEHQr-9oJ4tftkH-gTCowTAqwWSg,3686
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 aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py,sha256=CP4fKFU_JYP_AXvTptnwpjaVar1d5lVKV5vxYgH_1j4,5309
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