aiagents4pharma 1.42.0__py3-none-any.whl → 1.44.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py

@@ -1,13 +1,31 @@
 #!/usr/bin/env python3
 
-"""
-Tool for querying the metadata table of the last displayed papers.
 
-This tool loads the most recently displayed papers into a pandas DataFrame and uses an
-LLM-driven pandas agent to answer metadata-level questions (e.g., filter by author, list titles).
-It is intended for metadata exploration only, and does not perform content-based retrieval
-or summarization. For PDF-level question answering, use the 'question_and_answer_agent'.
 """
+Query the metadata table of the most recently displayed papers.
+
+This tool loads `state['last_displayed_papers']` into a pandas DataFrame and uses an
+LLM-driven DataFrame agent to execute metadata-level queries. It supports both
+natural-language prompts (e.g., “list titles by author X”) and direct Python expressions
+over the DataFrame.
+
+Capabilities
+- Filter, sort, and aggregate rows using metadata columns (e.g., Title, Authors, Venue, Year).
+- Extract paper identifiers from a designated column (default: 'paper_ids'),
+  optionally for a single row.
+- Return the DataFrame agent’s textual result as a ToolMessage.
+
+Requirements
+- `state['llm_model']`: model used to instantiate the DataFrame agent.
+- `state['last_displayed_papers']`: dictionary mapping row keys → metadata records.
+
+Notes
+- Operates strictly on the metadata table; it does not parse or read PDF content.
+- When `extract_ids=True`, the tool constructs a Python expression for the agent to evaluate
+  and return identifiers from `id_column`. If `row_number` is provided (1-based), only that row’s
+  first identifier is returned; otherwise a list is returned from all rows that have values.
+"""
+
 
 import logging
 from typing import Annotated, Optional, Any
@@ -32,23 +50,32 @@ class NoPapersFoundError(Exception):
 
 class QueryDataFrameInput(BaseModel):
     """
-    Pydantic schema for querying the metadata of displayed papers.
+    Input schema for querying the last displayed papers metadata DataFrame.
 
     Fields:
-      question: A free-text prompt or Python expression to query the papers DataFrame.
-      tool_call_id: LangGraph-injected identifier for tracking the tool invocation.
-      state: Agent state dictionary. Must include:
-        - 'last_displayed_papers': dictionary of paper metadata (rows = papers).
-        - 'llm_model': model used to instantiate the DataFrame agent.
-
-    Notes:
-      - This tool is only for metadata queries. It does not perform full-text PDF analysis.
-      - You can access standard metadata columns such as 'Title', 'Authors',
-        'Venue', 'Year', and the unified 'paper_ids' (list of <source>:<ID>).
-      - To extract raw paper IDs for downloading, set extract_ids=True and specify:
-          - id_column: 'paper_ids' (default)
-          - row_number: 1-based index of the paper to return (optional—for a single ID)
-        Example: {{"question":"","extract_ids":True,"row_number":4}}
+      question (str):
+        The query to execute. Accepts natural language (e.g., "List titles from 2024")
+        or a Python expression over the DataFrame (e.g., "df['Title'].tolist()").
+
+      extract_ids (bool, default=False):
+        When True, the tool prepares a Python expression for the DataFrame agent to extract
+        identifiers from `id_column`. Use to obtain IDs from the metadata table.
+
+      id_column (str, default="paper_ids"):
+        Name of the column that contains per-row lists of identifiers (e.g., ["arxiv:2301.12345"]).
+        Used only when `extract_ids=True`.
+
+      row_number (int | None, default=None):
+        1-based row index. When provided with `extract_ids=True`, returns only that row’s first
+        identifier. When omitted, returns a list of first identifiers from each applicable row.
+
+      tool_call_id (InjectedToolCallId):
+        Internal identifier for tracing the tool invocation.
+
+      state (dict):
+        Agent state containing:
+          - 'last_displayed_papers': dict with the current results table (rows → metadata)
+          - 'llm_model': model object or reference for the DataFrame agent
     """
 
     question: str = Field(
@@ -95,30 +122,55 @@ def query_dataframe(
     **kwargs: Any,
 ) -> Command:
     """
-    Perform a tabular query on the most recently displayed papers.
-
-    This function loads the last displayed papers into a pandas DataFrame and uses a
-    pandas DataFrame agent to answer metadata-level questions (e.g., "Which papers have
-    'Transformer' in the title?", "List authors of paper X"). It does not perform PDF
-    content analysis or summarization; for content-level question answering, use the
-    'question_and_answer_agent'.
-
-    Args:
-        question (str): The metadata query to ask over the papers table.
-        extract_ids (bool): If true, modify the query to instruct the DataFrame agent
-        to extract values from the specified ID column via Python code.
-        id_column (str): Name of the metadata column to extract values from when extract_ids=True.
-        row_number (int, optional): 1-based index of the ID to extract from the list; if provided,
-        returns only that single ID.
-        state (dict): The agent's state containing 'last_displayed_papers' key
-        referencing the metadata table in state.
-        tool_call_id (str): LangGraph-injected identifier for this tool call.
-
-    Returns:
-        Command: A structured response containing a ToolMessage with the query result.
-
-    Raises:
-        NoPapersFoundError: If no papers have been displayed yet.
+    Execute a metadata query against the DataFrame built from `last_displayed_papers`.
+
+    Behavior
+    - Builds a pandas DataFrame from `state['last_displayed_papers']`.
+    - Instantiates a pandas DataFrame agent with `state['llm_model']`.
+    - Runs either:
+        • the provided natural-language prompt, or
+        • a constructed Python expression when `extract_ids=True`
+          (optionally scoped to `row_number`, 1-based).
+    - Returns the DataFrame agent’s output text in a ToolMessage.
+
+    Parameters
+      question (str):
+        Natural-language query or Python expression to run on the DataFrame.
+      state (dict):
+        Must provide 'llm_model' and 'last_displayed_papers'.
+      tool_call_id (str):
+        Internal identifier for the tool call.
+      **kwargs:
+        extract_ids (bool): Enable ID extraction from `id_column`.
+        id_column (str): Column containing lists of identifiers (default: "paper_ids").
+        row_number (int | None): 1-based index for a single-row extraction.
+
+    Returns
+      Command:
+        update = {
+          "messages": [
+            ToolMessage(
+              content=<text result from the DataFrame agent>,
+              tool_call_id=<tool_call_id>
+            )
+          ]
+        }
+
+    Errors
+    - Raises `ValueError` if 'llm_model' is missing in `state`.
+    - Raises `NoPapersFoundError` if `state['last_displayed_papers']` is missing or empty.
+    - Raises `ValueError` if a required argument for the chosen mode is invalid
+      (e.g., no `id_column` when `extract_ids=True`).
+
+    Examples
+    - Natural language:
+        question="List titles where Year >= 2023"
+    - Python list of titles:
+        question="df.query('Year >= 2023')['Title'].tolist()"
+    - Extract first ID from row 1:
+        extract_ids=True, row_number=1
+    - Extract first IDs from all rows:
+        extract_ids=True
     """
     logger.info("Querying last displayed papers with question: %s", question)
     llm_model = state.get("llm_model")

aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py

@@ -1,12 +1,11 @@
 #!/usr/bin/env python3
 
 """
-Tool for retrieving a Semantic Scholar paper ID given a paper title.
+Resolve a paper title to a Semantic Scholar paperId.
 
-This tool queries the Semantic Scholar API for the best match of the provided paper title
-and returns the unique Semantic Scholar paperId. Use when you have a known title and need its
-Semantic Scholar identifier for further metadata retrieval or pipeline integration. Do not
-use this tool for broad literature search; use the `search` tool instead.
+This module provides a tool that queries the Semantic Scholar API for the best match to a
+given paper title (full or partial) and returns the corresponding `paperId` string.
+Configuration is loaded via Hydra and the top ranked result is returned.
 """
 
 import logging
@@ -27,11 +26,14 @@ logger = logging.getLogger(__name__)
 
 class RetrieveSemanticScholarPaperIdInput(BaseModel):
     """
-    Pydantic schema for retrieving a Semantic Scholar paper ID.
-
-    Fields:
-      paper_title: The title (full or partial) of the paper to look up on Semantic Scholar.
-      tool_call_id: LangGraph-injected identifier for tracking the tool invocation.
+    Input schema for title→paperId resolution.
+
+    Fields
+    -------
+    paper_title : str
+        Paper title to search. Accepts full titles or informative partial titles.
+    tool_call_id : InjectedToolCallId
+        Runtime-injected identifier for tracing the tool invocation.
     """
 
     paper_title: str = Field(
@@ -50,27 +52,43 @@ def retrieve_semantic_scholar_paper_id(
     tool_call_id: str,
 ) -> Command[Any]:
     """
-    Retrieve a Semantic Scholar paper ID using a paper title.
-
-    This tool searches Semantic Scholar for the best match to the provided paper title
-    and returns the corresponding unique paper ID. It is intended to support downstream
-    tasks such as recommendations, metadata lookups, or citation graph queries.
-
-    Use this tool when you know the full or partial title of a paper and need its
-    Semantic Scholar ID.
-    For broad literature searches or topic-based queries, use a general `search` tool instead.
-
-    Args:
-        paper_title (str): The full or partial title of the paper to look up.
-        tool_call_id (str): LangGraph-injected identifier for this tool call.
+    Look up a Semantic Scholar paperId from a paper title.
+
+    Behavior
+    --------
+    - Loads Hydra config from `tools.retrieve_semantic_scholar_paper_id`.
+    - Sends a search request with `query=<paper_title>`, `limit=1`, and requested fields.
+    - Parses the top hit and returns its `paperId` as the ToolMessage content (plain string).
+
+    Parameters
+    ----------
+    paper_title : str
+        Title or informative partial title to resolve.
+    tool_call_id : str
+        Runtime-injected identifier for the tool call.
+
+    Returns
+    -------
+    Command
+        update = {
+          "messages": [
+            ToolMessage(
+              content="<paperId>",  # Semantic Scholar paperId string
+              tool_call_id=<tool_call_id>
+            )
+          ]
+        }
 
-    Returns:
-        Command: A structured response containing a ToolMessage whose content is
-            the Semantic Scholar paper ID string (e.g., 'abc123xyz').
+    Exceptions
+    ----------
+    ValueError
+        Raised when no match is found for the provided title.
+    requests.RequestException
+        Raised on network/HTTP errors (timeout, connection issues, etc.).
 
-    Raises:
-        ValueError: If no matching paper is found for the given title.
-        requests.RequestException: If the API request fails.
+    Examples
+    --------
+    >>> retrieve_semantic_scholar_paper_id("Attention Is All You Need", "tc_123")
     """
     # Load hydra configuration
     with hydra.initialize(version_base=None, config_path="../../configs"):

{aiagents4pharma-1.42.0.dist-info → aiagents4pharma-1.44.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.42.0
+Version: 1.44.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -72,6 +72,7 @@ Dynamic: license-file
 <!--  Project Info -->
 
 ![RELEASE](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma?label=RELEASE)
+![Docker Compose Release Version](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma?label=Docker%20Compose%20Version)
 ![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)
 
 <!--  Deployment Workflows -->
@@ -79,6 +80,7 @@ Dynamic: license-file
 [![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
 [![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
 [![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
+[![Docker Compose Release](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml)
 
 <!--  Tests -->
 

{aiagents4pharma-1.42.0.dist-info → aiagents4pharma-1.44.0.dist-info}/RECORD

@@ -86,7 +86,7 @@ aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py,sha256=C1yyRZW8hq
 aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/default.yaml,sha256=Ua99yECXiwp4ZCUDgsDskYbKzcJrv7roQuLj31Zky4c,1037
 aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml,sha256=M4scS2KEgux24bWuepNyJLzTFZ-CagcF6zLCw-6JK3k,919
+aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/default.yaml,sha256=QEtxF7Fj1DYFEw1qS-JXAptbIgNHc-dnBV6aic0alkk,1330
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml,sha256=U8HvMsYbaOwDwQPATj7EFvLtTy7XZEplE5WMoNjgYYc,1469
 aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
@@ -109,7 +109,7 @@ aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_dataset.py,sha256=NFUls
 aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_primekg.py,sha256=Pvu0r93CpnhjkfMxc-EiVLpAJ04FdW9iTamCnetu654,2272
 aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_starkqa_primekg.py,sha256=TuIsqcN1Mww3DTqGk6ebgJBWzUWdMWEq2yRQuYSFqvA,4416
 aiagents4pharma/talk2knowledgegraphs/tests/test_tools_graphrag_reasoning.py,sha256=aOKHTber2Cg3mjNjfIa6RZU7XdFj5C2ps1YEUXw76CI,10650
-aiagents4pharma/talk2knowledgegraphs/tests/test_tools_milvus_multimodal_subgraph_extraction.py,sha256=ATD3KDK-WQHG3t480u6sZavfMN7rTZcnhcCoQnPRocY,18889
+aiagents4pharma/talk2knowledgegraphs/tests/test_tools_milvus_multimodal_subgraph_extraction.py,sha256=rS2QbSjzHB8TA7JX0K66boILoug9qCJSPp3lti_CL_s,27930
 aiagents4pharma/talk2knowledgegraphs/tests/test_tools_multimodal_subgraph_extraction.py,sha256=Da-hXcu41_5Ge4DPlOoY6OqBwYnXPc58Q89wuywqVJM,5806
 aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py,sha256=C2HzmAG1XCeV1hwZzz3-9_2dm_84-i1BvTNWA1pqUwM,5393
 aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_summarization.py,sha256=oBqfspXXOxH04OQuPb8BCW0liIQTGKXtaPNSrPpQtFc,7597
@@ -124,13 +124,13 @@ aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py,sha256=
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py,sha256=0SgYvqdvxseUYTHx2KuSNI2hnmQ3VVVz0F-79_-P41o,1769
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py,sha256=r1D74mavsnSCm4xnWl0n0nM9PZqgm3doD2dulNrKNVQ,1754
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py,sha256=G13Diw7cA5TGINUNO1CDnN4rM6KbepxRXNjuzY578DI,1611
-aiagents4pharma/talk2knowledgegraphs/tests/test_utils_extractions_milvus_multimodal_pcst.py,sha256=XlB39lhaCax1r5eAYdvaJqyWvxgG1MO8jKD4MWyuT68,7491
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_extractions_milvus_multimodal_pcst.py,sha256=uGo60iLGuXkkiG67JBbRjUPxw1uICxPYlenbb9wrD48,20893
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py,sha256=pal76wi7WgQWUNk56BrzfFV8jKpbDaHHdbwtgx_gXLI,2410
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py,sha256=31WPX8MrhnztoHUROAlH5KvHeXMbB_Jndp3ypAKJO9E,1543
 aiagents4pharma/talk2knowledgegraphs/tools/__init__.py,sha256=u50fnnIhm7NHt4JhQeXdF_XtNYR2i35p4VRNQzP1CVQ,268
 aiagents4pharma/talk2knowledgegraphs/tools/graphrag_reasoning.py,sha256=OEuOFncDRdb7TQEGq4rkT5On-jI-R7Nt8K5EBzaND8w,5338
 aiagents4pharma/talk2knowledgegraphs/tools/load_arguments.py,sha256=zhmsRp-8vjB5rRekqTA07d3yb-42HWqng9dDMkvK6hM,623
-aiagents4pharma/talk2knowledgegraphs/tools/milvus_multimodal_subgraph_extraction.py,sha256=eANDj6b6l9Oc5fOZxGx-PInd9YfD4_4sDFFPuzPkFNs,21945
+aiagents4pharma/talk2knowledgegraphs/tools/milvus_multimodal_subgraph_extraction.py,sha256=M-Rrg-mPpe0dpP-AF85tgLSJjPRqFv3UUs9cWTHcCes,24065
 aiagents4pharma/talk2knowledgegraphs/tools/multimodal_subgraph_extraction.py,sha256=Qjl8hXG8Gv5jQ4pBX8me0pGGakqRZmcDfTGgdEHD9pc,15394
 aiagents4pharma/talk2knowledgegraphs/tools/subgraph_extraction.py,sha256=te06QMFQfgJWrjaGrqpcOYeaV38jwm0KY_rXVSMHkeI,11468
 aiagents4pharma/talk2knowledgegraphs/tools/subgraph_summarization.py,sha256=mDSBOxopDfNhEJeU8fVI8b5lXTYrRzcc97aLbFgYSy4,4413
@@ -151,42 +151,38 @@ aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py,sha256
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/reactome_pathways.py,sha256=I0cD0Fk2Uk27_4jEaIhpoGhoMh_RphY1VtkMnk4dkPg,2011
 aiagents4pharma/talk2knowledgegraphs/utils/enrichments/uniprot_proteins.py,sha256=z0Jb3tt8VzRjzqI9oVcUvRlPPg6BUdmslfKDIEFE_h8,3013
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=6xVclMlSuAIHQXBvn5D9zRLDzSv2LWLcAwDQw-nwZgM,153
-aiagents4pharma/talk2knowledgegraphs/utils/extractions/milvus_multimodal_pcst.py,sha256=peFGn9XXpE7H9leVqQHc2Ec7x2ZRiehYkcCCCNo3b_E,16415
+aiagents4pharma/talk2knowledgegraphs/utils/extractions/milvus_multimodal_pcst.py,sha256=-Qi35E4Yev0jv6UhAhhVkgaF53p2zvmS6FMytOOx-Xs,21533
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/multimodal_pcst.py,sha256=Irh5JXEhaLZ6Rxv3h5Anif_rGNItyLOGDWg1RACmoDA,12628
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=NOZxTklAH1j1ggu97Ib8Xn9LCKudEWt-8dx8w7yxVD8,180
 aiagents4pharma/talk2scholars/agents/__init__.py,sha256=c_0Pk85bt-RfK5RMyALM3MXo3qXVMoYS7BOqM9wuFME,317
 aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=oQqa1z4nvfUvPWCX-SUHGs9jOCJKtzjw86jXJZ68gCk,3382
-aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=J_kEl8joQfM80211xlNLZA9RkN52fY58dbCisuiEft8,3687
+aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=gIaaUcT4JPuQSJ5C-PPtY92oskWKh69zl99WzqPO9AA,3501
 aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=GEXzJMQxIeZ7zLP-AlnTMU-n_KXZ7g22Qd9L3USIc_4,3626
 aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=oui0CMSyXmBGBJ7LnYq8Ce0V8Qc3BS6GgH5Qx5wI6oM,4565
 aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=NAmEURIhH-sjXGO-dqAigUA10m-Re9Qe1hY8db4CIP0,4370
 aiagents4pharma/talk2scholars/configs/__init__.py,sha256=Y9-4PxsNCMoxyyQgDSbPByJnO9wnyem5SYL3eOZt1HY,189
-aiagents4pharma/talk2scholars/configs/config.yaml,sha256=F7BCgmcnhfkyKT6qFL11E_iwTYPmF8W_0b1n4KAaSho,680
+aiagents4pharma/talk2scholars/configs/config.yaml,sha256=GyL69HPuoccv93Gcw7S44xiWG-iPxfKU-p27VWC12iY,590
 aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=plv5Iw34gvbGZbRyJapvoOiiFXekRQIwjV_yy5AR_SI,104
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=D94LW4cXLmJe4dNl5qoR9QN0JnBqGLbQDgDLqhCNUE0,213
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=hew5vyrhLeJktoN6DTPRRpnINrXqKZ4trLJQDOuDGOA,4712
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=vSxteufVdgZeXBnU_LhduoBNBVz17s3mpqrjFw-QPUI,3677
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml,sha256=D-IanUKvd2yhrFJjQCMnIG8UNQ3fbkW_bOdhHWRKmq8,357
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/default.yaml,sha256=S1cmJaX6Xp4i_ixExZfP0qgD-tXQVFbpWpXvrh7ZVeQ,1173
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml,sha256=p3hFJi-1xbHCNagTG13WHvsrPt11XQg1nHS7VJx2XOY,166
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/default.yaml,sha256=MYC9REeARVfTOCWyV_4cInvWHDksKMz193Q1LirKtZw,832
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=CHMsW3cpGtfYWpSIY5XgNEYPvbI31OjOYfl_VbbKIyY,707
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=X88qKa0DgqCIvpnJgO_qEqAhhT9ymDr1B8HkJLTkB0U,2718
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=FUbJIiH_FHeL0n1M-HSsLX_R2gMBRxBnPcejhd0HrYc,399
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=d_38r0JtOPW0wM3J7LTB17aW3eBRyA6nFhB8MJd6lOw,1016
 aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=tXpOW3R4eAfNoqvoaHfabSG-DcMHmUGSTg_4zH_vlgw,94
 aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=A6nYjrgzEyRv5JYsGN7oqNX4-tufMBZ6mg-A7bMX6V4,906
 aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=6pHPF0ZGY78SD6KPMukd_xrfO1ocVXcyrsrB-kz-OnI,402
-aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml,sha256=VT3f-E6QGtqUjLEX0eaw9b_7f1Fp83cnnMOpqOufK4I,120
-aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml,sha256=d5_dl1_FYWseBGTVGkvC41jfJMsMUaDMOmC_av3aL4Q,72
-aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml,sha256=NaWmyVZ71rIF3ZRUm912wQgRL0cgDTWA-hVKeu60rtg,70
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=comNgL9hRpH--IWuEsrN6hV5WdrJmh-ZsRh7hbryVhg,631
+aiagents4pharma/talk2scholars/configs/tools/paper_download/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
+aiagents4pharma/talk2scholars/configs/tools/paper_download/default.yaml,sha256=KaHKlCf-Y1Ob1wnEKhfhKEaLye_L9Qs_BT3PhLlDM6Y,3571
 aiagents4pharma/talk2scholars/configs/tools/question_and_answer/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/question_and_answer/default.yaml,sha256=Pa3JVyA9tabXZ4Bk3n5dAml7P-nXUcT7HgkA8Kr_sXk,2238
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
@@ -202,12 +198,14 @@ aiagents4pharma/talk2scholars/configs/tools/zotero_write/default.yaml,sha256=gB7
 aiagents4pharma/talk2scholars/state/__init__.py,sha256=ReScKLpEvedq4P6ww52NRQS0Xr6SSQV7hqoQ83Mt75U,138
 aiagents4pharma/talk2scholars/state/state_talk2scholars.py,sha256=Z2zV-SXB2SMnn8PnjWjmK-OD5KjUwMTChBpXBAcl2hg,3885
 aiagents4pharma/talk2scholars/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
+aiagents4pharma/talk2scholars/tests/test_arxiv_downloader.py,sha256=JvqMLUeNVnmkhGo9fjDr73r76kwWFiuBbJHMAdo7Jko,18772
+aiagents4pharma/talk2scholars/tests/test_base_paper_downloader.py,sha256=Rtp05inMVbDg4Yt7HlmXFt3_9xOXUighQsxishmABSk,25107
+aiagents4pharma/talk2scholars/tests/test_biorxiv_downloader.py,sha256=qvNDcJTpqV7L5bZ3r40wtBehNcrDNtlOJLkzhSNh6q0,27690
 aiagents4pharma/talk2scholars/tests/test_main_agent.py,sha256=4Z3xLq8MGlayGhQE5qKOirYotwJrlf7fk8rqAaORorg,7617
+aiagents4pharma/talk2scholars/tests/test_medrxiv_downloader.py,sha256=aoLB64tw7HXMv0xIIOUZ5CFt9fd8n61kQMmKpznh2M0,20848
 aiagents4pharma/talk2scholars/tests/test_nvidia_nim_reranker.py,sha256=ftfn4VenufZ-zt2nSOyOoCjfSbwFOW9CS1DLzPtBEaM,4410
-aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py,sha256=gKSQp-sw62FplNnGYW0wv2ZIUEefh3o0tFWbRzy9yLs,5068
-aiagents4pharma/talk2scholars/tests/test_paper_download_biorxiv.py,sha256=gosuW4VBXyorQXbf0TpgAIT2hQjEeuvTTnT1jnoBYqM,6405
-aiagents4pharma/talk2scholars/tests/test_paper_download_medrxiv.py,sha256=iNq9vEIVapmnUZTRJXCv_UoaWThGapW7Vt_2BmZG9NE,6414
-aiagents4pharma/talk2scholars/tests/test_paper_download_tools.py,sha256=lGXbHl3lEXDjMHAX9uCgrREBOUuOHWv9TsYEshiG_tc,10421
+aiagents4pharma/talk2scholars/tests/test_paper_download_agent.py,sha256=1QeIf9SrBM712DOPC5qotL-vDo7Ax-9l9LDDEtTJNdI,5344
+aiagents4pharma/talk2scholars/tests/test_paper_downloader.py,sha256=8r_OZOJkHZ8mhrSNuSZ3aLyIA6Ngb-S23S30XmYRZ-c,22822
 aiagents4pharma/talk2scholars/tests/test_pdf_agent.py,sha256=9Kr0FcyFWmUDTasYh6ZdS-OWQqy37mH9K3p5Y0dqQHw,4283
 aiagents4pharma/talk2scholars/tests/test_pdf_answer_formatter.py,sha256=a1a_z1M9sOQ_SFo-gHM3xA_f5MoJJmEoW8Tc3AX9vL0,2239
 aiagents4pharma/talk2scholars/tests/test_pdf_batch_processor.py,sha256=e8KQJ80nbOmCH4mgDnIXXjlrRk0zf0g-5Odt2jsCU0s,3251
@@ -221,6 +219,7 @@ aiagents4pharma/talk2scholars/tests/test_pdf_retrieve_chunks.py,sha256=2cjbCrf86
 aiagents4pharma/talk2scholars/tests/test_pdf_singleton_manager.py,sha256=gOk8L9wNRPUnAiB89n1a4pQQPI7UtonRi7-IcCip94k,5628
 aiagents4pharma/talk2scholars/tests/test_pdf_vector_normalization.py,sha256=pu9I3tromjToIN5r4S8sWanaLBVhhk71UPP5zTTGwZY,3928
 aiagents4pharma/talk2scholars/tests/test_pdf_vector_store.py,sha256=-7CUiPLT4mOBVkNV2qlF7t4yU_mRArM0uAcUAKgEY4k,15644
+aiagents4pharma/talk2scholars/tests/test_pubmed_downloader.py,sha256=FpuyL2NhlnX6tkI8UwU7rxYJe94TdHlwJWZan5rbXcg,44972
 aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py,sha256=UKSD7wLJ1cZunw8a1BHM7E-NUML6blxpqoDroCYuvQs,4245
 aiagents4pharma/talk2scholars/tests/test_read_helper_utils.py,sha256=yTT1aLpTydDSdGcRZur5cMktwYZbFK5NEUgOBvltcWg,3819
 aiagents4pharma/talk2scholars/tests/test_s2_agent.py,sha256=TsdNlZ6vHz18bbX6Vto28nbBLRDI94wSFt5-1acDK64,7768
@@ -240,10 +239,14 @@ aiagents4pharma/talk2scholars/tests/test_zotero_pdf_downloader_utils.py,sha256=N
 aiagents4pharma/talk2scholars/tests/test_zotero_read.py,sha256=qkudWMjxjjTYKJ1zvpWs0EJXCIvFx-iNKyKs_Tv1CSI,29061
 aiagents4pharma/talk2scholars/tests/test_zotero_write.py,sha256=qWlO0XoZJ6vxUxgisjYv9Np87CoTEDxiQBEOhdj9foo,6111
 aiagents4pharma/talk2scholars/tools/__init__.py,sha256=c8pYHDqR9P0Frz2jWjbvyizfSTBMlMFzGsiQzx2KC9c,189
-aiagents4pharma/talk2scholars/tools/paper_download/__init__.py,sha256=Lu5FmBxDH8mIIYE41G8_BKYXUf-vHIYVwujidbeydl4,295
-aiagents4pharma/talk2scholars/tools/paper_download/download_arxiv_input.py,sha256=e3S8JusJVVSEC_tFh8H5CS9ZqD20jX8hkFO9EYESBXo,5653
-aiagents4pharma/talk2scholars/tools/paper_download/download_biorxiv_input.py,sha256=Iipvv0P-KLbW8ELMDBLr-FxgoGBjRjPToVw7pBVJS-Y,3676
-aiagents4pharma/talk2scholars/tools/paper_download/download_medrxiv_input.py,sha256=2ONhx7rygCACf_SYc1cxDAmQP4ZzkB39OoLZYsbFMyI,3752
+aiagents4pharma/talk2scholars/tools/paper_download/__init__.py,sha256=PzJTrcXBHB3e2rgOvJ3Q8JJjvZAXyUCtGcGdANk1svE,227
+aiagents4pharma/talk2scholars/tools/paper_download/paper_downloader.py,sha256=YJuuRhkxFZIHyQTE3Hh4rkJF1hYCFNgORd_9dyp9-5E,16908
+aiagents4pharma/talk2scholars/tools/paper_download/utils/__init__.py,sha256=mbtb0IK6fW6ASQyqMhkaCHFBXQUguR7G6hZHrTJwZXc,467
+aiagents4pharma/talk2scholars/tools/paper_download/utils/arxiv_downloader.py,sha256=xWb4YPbDPZbgBDS1INDCSrOVeNiDRNC2KYhiOQjJV3o,7029
+aiagents4pharma/talk2scholars/tools/paper_download/utils/base_paper_downloader.py,sha256=pIt-BFgt7mh4XPXzcfRy5LY8xzmhADF6j8-TOyiaa1Q,11350
+aiagents4pharma/talk2scholars/tools/paper_download/utils/biorxiv_downloader.py,sha256=sz4lc1jQEKzYk9kX2QJotgjbNWXpLfmi8jfY-zVW8Wg,11652
+aiagents4pharma/talk2scholars/tools/paper_download/utils/medrxiv_downloader.py,sha256=9jKbh6lW9IBI9RJhHzqV1ktz3LfvoD3B5ayeXk15Eg4,6638
+aiagents4pharma/talk2scholars/tools/paper_download/utils/pubmed_downloader.py,sha256=Md9bWaiy7_88NIue_3NkPrmXyNZQS8zLcK4xaFQmIjU,12177
 aiagents4pharma/talk2scholars/tools/pdf/__init__.py,sha256=DPpOfON3AySko5EBBAe_3udOoSaAdQWNyGeNvJyV5R8,138
 aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py,sha256=_HLO04bzTSlnEEWwkJ3rC9Gjz8MPeHVglqovoTDOSp4,5844
 aiagents4pharma/talk2scholars/tools/pdf/utils/__init__.py,sha256=AlvoJY0hI4MCS4zHO3EtFkFJpKqjO7ZxWkoE3QvHi88,820
@@ -265,8 +268,8 @@ aiagents4pharma/talk2scholars/tools/pdf/utils/vector_store.py,sha256=X9OGwV3RHZI
 aiagents4pharma/talk2scholars/tools/s2/__init__.py,sha256=w_eiw0pG8HNp79F9O_icXs_Yl_4odsmagYNKDTjIsvk,428
 aiagents4pharma/talk2scholars/tools/s2/display_dataframe.py,sha256=qnY7AQDnAs0SrmV7AZ9pWm10HEmPlO7EBfzYvpb3jvs,3965
 aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=TEt4jOX1u8v3w_u10sGx-Ghwhe4yjuaYmUjD62nJQJM,3886
-aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py,sha256=EJ-EV-pk2kLS12Q5HatBdGue3t-MB8mx5PrSxtLN7Co,7042
-aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=0yILvpqraXldd61nLHSCfITvKyLIxts6HBC5GaGVfBQ,3995
+aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py,sha256=bZiSe7-hf0IHIoZhITtgOSDauyd9NAtim5ukWi1vyuA,8599
+aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=zwm4LGfFWxJLIPRc2TO5zQ48kCKe7EmkwY1SyTVCTAg,4014
 aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=SUAN32x1d9dNikFKitcXZZ0BhFfsGMdLDk0z0DpJXuA,3334
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=JTggOB4sqhTF1kP81Gl_54RjpbHIfqtJEoUTxlZ82N8,3630
 aiagents4pharma/talk2scholars/tools/s2/utils/__init__.py,sha256=wBTPVgiXbmIJUMouOQRwojgk5PJXeEinDJzHzEToZbU,229
@@ -283,8 +286,8 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9y
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=ERBha8afU6Q1EaRBe9qB8tchOzZ4_KfFgDW6EElOJoU,4816
-aiagents4pharma-1.42.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.42.0.dist-info/METADATA,sha256=qbfg8yUF-3Tn5k82Ry5wCuLNzv6PWVpeL46inguNRuI,12894
-aiagents4pharma-1.42.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aiagents4pharma-1.42.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.42.0.dist-info/RECORD,,
+aiagents4pharma-1.44.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.44.0.dist-info/METADATA,sha256=Ibu0QQcsmO9c65SO-Q5jkhU2Vd-QXCQ5fS9h-2Hoa6I,13281
+aiagents4pharma-1.44.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aiagents4pharma-1.44.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.44.0.dist-info/RECORD,,

aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/default.yaml

@@ -1,4 +0,0 @@
-api_url: "http://export.arxiv.org/api/query"
-request_timeout: 10
-chunk_size: 1024
-pdf_base_url: "https://arxiv.org/pdf"

aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/__init__.py

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

aiagents4pharma/talk2scholars/configs/tools/download_biorxiv_paper/default.yaml

@@ -1,2 +0,0 @@
-api_url: "https://api.biorxiv.org/details/biorxiv/"
-request_timeout: 20

aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/__init__.py

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

aiagents4pharma/talk2scholars/configs/tools/download_medrxiv_paper/default.yaml

@@ -1,2 +0,0 @@
-api_url: "https://api.biorxiv.org/details/medrxiv"
-request_timeout: 20