aiagents4pharma 1.36.0__py3-none-any.whl → 1.38.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (36) hide show
  1. aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py +12 -4
  2. aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py +2 -2
  3. aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +7 -6
  4. aiagents4pharma/talk2knowledgegraphs/configs/config.yaml +1 -0
  5. aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py +0 -0
  6. aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py +1 -0
  7. aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py +12 -11
  8. aiagents4pharma/talk2knowledgegraphs/tests/test_tools_multimodal_subgraph_extraction.py +152 -0
  9. aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py +36 -65
  10. aiagents4pharma/talk2knowledgegraphs/tools/__init__.py +1 -0
  11. aiagents4pharma/talk2knowledgegraphs/tools/multimodal_subgraph_extraction.py +374 -0
  12. aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py +1 -0
  13. aiagents4pharma/talk2knowledgegraphs/utils/extractions/multimodal_pcst.py +292 -0
  14. aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml +1 -0
  15. aiagents4pharma/talk2scholars/state/state_talk2scholars.py +33 -7
  16. aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py +59 -3
  17. aiagents4pharma/talk2scholars/tests/test_read_helper_utils.py +110 -0
  18. aiagents4pharma/talk2scholars/tests/test_s2_display.py +20 -1
  19. aiagents4pharma/talk2scholars/tests/test_s2_query.py +17 -0
  20. aiagents4pharma/talk2scholars/tests/test_state.py +25 -1
  21. aiagents4pharma/talk2scholars/tests/test_zotero_pdf_downloader_utils.py +46 -0
  22. aiagents4pharma/talk2scholars/tests/test_zotero_read.py +35 -40
  23. aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py +62 -40
  24. aiagents4pharma/talk2scholars/tools/s2/display_dataframe.py +6 -2
  25. aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py +2 -1
  26. aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py +7 -3
  27. aiagents4pharma/talk2scholars/tools/s2/search.py +2 -1
  28. aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py +2 -1
  29. aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py +79 -136
  30. aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py +147 -0
  31. aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py +42 -9
  32. {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/METADATA +2 -1
  33. {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/RECORD +36 -29
  34. {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/WHEEL +1 -1
  35. {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/licenses/LICENSE +0 -0
  36. {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/top_level.txt +0 -0
@@ -1,7 +1,11 @@
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  #!/usr/bin/env python3
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  """
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- This tool is used to search for papers in Zotero library.
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+ Zotero Read Tool
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+
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+ This LangGraph tool searches a user's Zotero library for items matching a query
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+ and optionally downloads their PDF attachments. It returns structured metadata
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+ for each found item and makes the results available as an artifact.
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  """
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  import logging
@@ -20,7 +24,15 @@ logger = logging.getLogger(__name__)
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  class ZoteroSearchInput(BaseModel):
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- """Input schema for the Zotero search tool."""
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+ """Input schema for the Zotero search tool.
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+
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+ Attributes:
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+ query (str): Search string to match against item metadata.
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+ only_articles (bool): If True, restrict results to 'journalArticle' and similar types.
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+ limit (int): Maximum number of items to fetch from Zotero.
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+ download_pdfs (bool): If True, download PDF attachments for each item.
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+ tool_call_id (str): Internal identifier for this tool invocation.
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+ """
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  query: str = Field(
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  description="Search query string to find papers in Zotero library."
@@ -32,6 +44,10 @@ class ZoteroSearchInput(BaseModel):
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  limit: int = Field(
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  default=2, description="Maximum number of results to return", ge=1, le=100
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  )
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+ download_pdfs: bool = Field(
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+ default=False,
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+ description="Whether to download PDF attachments immediately (default True).",
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+ )
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  tool_call_id: Annotated[str, InjectedToolCallId]
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@@ -41,20 +57,36 @@ def zotero_read(
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  only_articles: bool,
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  tool_call_id: Annotated[str, InjectedToolCallId],
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  limit: int = 2,
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+ download_pdfs: bool = False,
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  ) -> Command[Any]:
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  """
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- Use this tool to search and retrieve papers from Zotero library.
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+ Execute a search on the Zotero library and return matching items.
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  Args:
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- query (str): The search query string to find papers.
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- tool_call_id (Annotated[str, InjectedToolCallId]): The tool call ID.
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- limit (int, optional): The maximum number of results to return. Defaults to 2.
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+ query (str): Text query to search in titles, abstracts, tags, etc.
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+ only_articles (bool): When True, only include items of type 'journalArticle'
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+ or 'conferencePaper'.
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+ tool_call_id (str): Internal ID injected by LangGraph to track this tool call.
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+ limit (int, optional): Max number of items to return (1–100). Defaults to 2.
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+ download_pdfs (bool, optional): If True, PDFs for each returned item will be downloaded now.
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+ If False, only metadata is fetched. Defaults to False.
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  Returns:
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- Dict[str, Any]: The search results and related information.
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+ Command[Any]: A LangGraph Command updating the agent state:
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+ - 'article_data': dict mapping item keys to metadata (and 'pdf_url' if downloaded).
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+ - 'last_displayed_papers': identifier pointing to the articles in state.
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+ - 'messages': list containing a ToolMessage with a human-readable summary
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+ and an 'artifact' referencing the raw article_data.
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  """
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  # Create search data object to organize variables
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- search_data = ZoteroSearchData(query, only_articles, limit, tool_call_id)
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+ # download_pdfs flag controls whether PDFs are fetched now or deferred
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+ search_data = ZoteroSearchData(
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+ query=query,
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+ only_articles=only_articles,
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+ limit=limit,
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+ download_pdfs=download_pdfs,
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+ tool_call_id=tool_call_id,
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+ )
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  # Process the search
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  search_data.process_search()
@@ -63,7 +95,8 @@ def zotero_read(
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  return Command(
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  update={
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  "article_data": results["article_data"],
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- "last_displayed_papers": "article_data",
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+ # Store the latest article_data mapping directly for display
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+ "last_displayed_papers": results["article_data"],
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  "messages": [
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  ToolMessage(
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  content=results["content"],
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: aiagents4pharma
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- Version: 1.36.0
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+ Version: 1.38.0
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  Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
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  Classifier: Programming Language :: Python :: 3
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  Classifier: License :: OSI Approved :: MIT License
@@ -62,6 +62,7 @@ Requires-Dist: umap-learn==0.5.7
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  Requires-Dist: plotly-express==0.4.1
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  Requires-Dist: seaborn==0.13.2
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  Requires-Dist: scanpy==1.11.0
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+ Requires-Dist: openpyxl==3.1.5
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  Dynamic: license-file
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  [![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
@@ -9,7 +9,7 @@ aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml,sha2
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  aiagents4pharma/talk2aiagents4pharma/states/__init__.py,sha256=3wSvCpM29oqvVjhbhabm7FNm9Zt0rHO5tEn63YW6doc,108
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  aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py,sha256=NxujEBDKubvpV9UG7ERTDRB6psr0XnObCNHyztLAhgo,485
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  aiagents4pharma/talk2aiagents4pharma/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
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- aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py,sha256=ndHQT4ycWy-uKRAND7JmX_SuNg4g9hJw4UCW0CbKSp0,4165
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+ aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py,sha256=_zUm8i8vrBbcDgpwExa1sVGr1A9FgZFuwoLS395RnhU,4418
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  aiagents4pharma/talk2biomodels/__init__.py,sha256=1cq1HX2xoi_a0nDPuXYoSTrnL26OHQBW3zXNwwwjFO0,181
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  aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
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  aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=g0DIW5P-dtJoVyG4weFdDgTrJPL_Dx1MMbTWextJDZ4,3455
@@ -73,17 +73,18 @@ aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=6q59gh_NQai
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  aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=MLe-twtFnOu-P8P9diYq7jvHBHbWFRRCZLcfpUzqPMg,2806
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  aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=Z0Eo7LTiKk0STsr8VI7wkCLq7PHrK1vYlH4I1hSNLiA,165
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  aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=iOAzuy_8A03tQDFtSBhC9dldUo62z5gfxcVtXAdLOJs,92
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- aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=IcXSZ2qQA1m-gS-o0Pj_g1oar8uPdhsbaovloUFka3Q,3058
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+ aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=w4wSSQ9gw_fzpcHZ2Bnqok17YDkFeQ3d72JenvQm6Oc,3089
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  aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=4_DVdpahaJ55yPl0aZotlFA_MYWLFF2cubWyKtBVI_Q,126
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- aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=X91262b-wkygiH4HrEr0bIzHxHDuDWwuxLQAmdUe-E4,367
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+ aiagents4pharma/talk2knowledgegraphs/configs/config.yaml,sha256=-AJXKnR2z5ig0SK_3vLL9JFjNRri7q7blHYFWxoTDl0,417
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  aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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  aiagents4pharma/talk2knowledgegraphs/configs/agents/t2kg_agent/default.yaml,sha256=ENCGROwYFpR6g4QD518h73sshdn3vPVpotBMk1QJcpU,4830
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  aiagents4pharma/talk2knowledgegraphs/configs/app/__init__.py,sha256=fKfc3FR7g5KjY9b6jzrU6cwKTVVpkoVZQS3dvUowu34,69
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  aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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- aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml,sha256=4azC4cH-_-zt-bRVgNjkFM24mjNke6Rgn9pNl7XWrPQ,912
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+ aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml,sha256=WJgd2ZU7_WQ1qlcTfkFlM8u23sH6eU2KgAm0E4kqqfs,941
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  aiagents4pharma/talk2knowledgegraphs/configs/tools/__init__.py,sha256=C1yyRZW8hqWw46p_bh1vAJp2z9aVvn4HpKjKkjlWIqY,150
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  aiagents4pharma/talk2knowledgegraphs/configs/tools/graphrag_reasoning/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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+ aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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@@ -94,15 +95,16 @@ aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py,sha256=-LaPLse8BkALqwFe
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  aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py,sha256=KBMhCJ7yjMWqQJJctFYdpjYAlwv48Jl6i1dddXP4f08,7599
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  aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py,sha256=Y-6-nORsnBJlU6rH0skyfr9S9J4PfTWK-af_p5UuknQ,7483
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  aiagents4pharma/talk2knowledgegraphs/states/__init__.py,sha256=XaqorSvx634dWRRlXUdzlisHtYMyqgJ2q7TanzsKlhw,108
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- aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py,sha256=6HqGo-awqoyNJG0igm5so5A4Tq8RPkCsjPg8Go38csE,1066
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+ aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py,sha256=y5bp6yObN-AQtTq-m8ml7UnZaeKYUiPV_yjskAzBJaI,1087
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  aiagents4pharma/talk2knowledgegraphs/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py,sha256=CCN6cyhEaiXSvIC-4y3ueDSzjDCBYDsmSmOor-DMeF4,3928
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+ aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py,sha256=PPfHKnfqMbUOBKU7q4VbQvHQymX1M_zTYdysQgVxKCs,3851
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  aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_biobridge_primekg.py,sha256=crH0eFA3P8P6IYzi1UWNa4YvRVrtlBzoScf9NaE1lDk,9827
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- aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py,sha256=zRi2j9Dm3VFywhhrPjVoJ7z_zJpAEM74MJRXapnhwVE,6246
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+ aiagents4pharma/talk2knowledgegraphs/tests/test_tools_multimodal_subgraph_extraction.py,sha256=Da-hXcu41_5Ge4DPlOoY6OqBwYnXPc58Q89wuywqVJM,5806
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+ aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py,sha256=C2HzmAG1XCeV1hwZzz3-9_2dm_84-i1BvTNWA1pqUwM,5393
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  aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py,sha256=G13Diw7cA5TGINUNO1CDnN4rM6KbepxRXNjuzY578DI,1611
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- aiagents4pharma/talk2knowledgegraphs/tools/__init__.py,sha256=zpD4h7EYtyq0QNOqLd6bkxrPlPb2XN64ceI9ncgESrA,171
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+ aiagents4pharma/talk2knowledgegraphs/tools/__init__.py,sha256=uleTEbhgvlYw4fOqV4NmoFvxGTon2Oim7jTQ5qPmYoU,216
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+ aiagents4pharma/talk2knowledgegraphs/tools/multimodal_subgraph_extraction.py,sha256=Qjl8hXG8Gv5jQ4pBX8me0pGGakqRZmcDfTGgdEHD9pc,15394
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@@ -138,7 +141,8 @@ aiagents4pharma/talk2knowledgegraphs/utils/enrichments/ols_terms.py,sha256=xSPP-
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- aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtfzKhB8GuOBD47XRi0NprwEXkOzwNl5eeu-hDTI,86
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+ aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=5bt3H6gGSAwN2K-IG7AHwG2lC4yQeMd2_jbhu2z5XKg,116
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+ aiagents4pharma/talk2knowledgegraphs/utils/extractions/multimodal_pcst.py,sha256=Irh5JXEhaLZ6Rxv3h5Anif_rGNItyLOGDWg1RACmoDA,12628
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+ aiagents4pharma/talk2scholars/tests/test_zotero_pdf_downloader_utils.py,sha256=N9CBRG0rQyqptKRCaYCH2VJk87O-wc9Cc1KI5MMnyjA,1670
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+ aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=p86RLy_9bMxm3KTDL2L0Ilb3yeF4K6IIkZCgbt4CsiE,2529
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+ aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py,sha256=Fgv7PIkIlRqfl8EprcXqr1S4wtbSG8itv7x-3nMf3Rc,3990
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+ aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py,sha256=54SO05iuJ2VHLJ1d4b16oh5b5VCp2-nB1nT5eOCHb-g,11712
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- aiagents4pharma-1.36.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
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- aiagents4pharma-1.36.0.dist-info/METADATA,sha256=4S4eCTvL7mAxQUmSDp4SIyn2WAYuOivLpcCdL-j5dGQ,16757
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- aiagents4pharma-1.36.0.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
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- aiagents4pharma-1.36.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
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- aiagents4pharma-1.36.0.dist-info/RECORD,,
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+ aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=ERBha8afU6Q1EaRBe9qB8tchOzZ4_KfFgDW6EElOJoU,4816
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+ aiagents4pharma-1.38.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
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+ aiagents4pharma-1.38.0.dist-info/METADATA,sha256=pHbuNJmxv1gfi0JcUnBxOMTcniqA4rMFEJfqgzwLFjw,16788
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+ aiagents4pharma-1.38.0.dist-info/RECORD,,
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (80.4.0)
2
+ Generator: setuptools (80.8.0)
3
3
  Root-Is-Purelib: true
4
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  Tag: py3-none-any
5
5