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.
- aiagents4pharma/talk2aiagents4pharma/tests/test_main_agent.py +12 -4
- aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py +2 -2
- aiagents4pharma/talk2knowledgegraphs/configs/app/frontend/default.yaml +7 -6
- aiagents4pharma/talk2knowledgegraphs/configs/config.yaml +1 -0
- aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py +0 -0
- aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py +1 -0
- aiagents4pharma/talk2knowledgegraphs/tests/test_agents_t2kg_agent.py +12 -11
- aiagents4pharma/talk2knowledgegraphs/tests/test_tools_multimodal_subgraph_extraction.py +152 -0
- aiagents4pharma/talk2knowledgegraphs/tests/test_tools_subgraph_extraction.py +36 -65
- aiagents4pharma/talk2knowledgegraphs/tools/__init__.py +1 -0
- aiagents4pharma/talk2knowledgegraphs/tools/multimodal_subgraph_extraction.py +374 -0
- aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py +1 -0
- aiagents4pharma/talk2knowledgegraphs/utils/extractions/multimodal_pcst.py +292 -0
- aiagents4pharma/talk2scholars/configs/tools/zotero_read/default.yaml +1 -0
- aiagents4pharma/talk2scholars/state/state_talk2scholars.py +33 -7
- aiagents4pharma/talk2scholars/tests/test_question_and_answer_tool.py +59 -3
- aiagents4pharma/talk2scholars/tests/test_read_helper_utils.py +110 -0
- aiagents4pharma/talk2scholars/tests/test_s2_display.py +20 -1
- aiagents4pharma/talk2scholars/tests/test_s2_query.py +17 -0
- aiagents4pharma/talk2scholars/tests/test_state.py +25 -1
- aiagents4pharma/talk2scholars/tests/test_zotero_pdf_downloader_utils.py +46 -0
- aiagents4pharma/talk2scholars/tests/test_zotero_read.py +35 -40
- aiagents4pharma/talk2scholars/tools/pdf/question_and_answer.py +62 -40
- aiagents4pharma/talk2scholars/tools/s2/display_dataframe.py +6 -2
- aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py +2 -1
- aiagents4pharma/talk2scholars/tools/s2/query_dataframe.py +7 -3
- aiagents4pharma/talk2scholars/tools/s2/search.py +2 -1
- aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py +2 -1
- aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py +79 -136
- aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py +147 -0
- aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py +42 -9
- {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/METADATA +2 -1
- {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/RECORD +36 -29
- {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/WHEEL +1 -1
- {aiagents4pharma-1.36.0.dist-info → aiagents4pharma-1.38.0.dist-info}/licenses/LICENSE +0 -0
- {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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Zotero Read Tool
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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
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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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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."
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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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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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Execute a search on the Zotero library and return matching items.
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Args:
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query (str):
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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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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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# 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()
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return Command(
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update={
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"article_data": results["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"],
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Metadata-Version: 2.4
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Name: aiagents4pharma
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Version: 1.
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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
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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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[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
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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=
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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
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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=
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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
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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=
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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/graphrag_reasoning/default.yaml,sha256=Ua99yECXiwp4ZCUDgsDskYbKzcJrv7roQuLj31Zky4c,1037
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aiagents4pharma/talk2knowledgegraphs/configs/tools/multimodal_subgraph_extraction/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_extraction/default.yaml,sha256=U8HvMsYbaOwDwQPATj7EFvLtTy7XZEplE5WMoNjgYYc,1469
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aiagents4pharma/talk2knowledgegraphs/configs/tools/subgraph_summarization/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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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=
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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=
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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_datasets_dataset.py,sha256=NFUlsZvhfIrkF4YenWfahrLK93Xhm5UYEGG_uYN2LVM,566
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aiagents4pharma/talk2knowledgegraphs/tests/test_datasets_starkqa_primekg.py,sha256=TuIsqcN1Mww3DTqGk6ebgJBWzUWdMWEq2yRQuYSFqvA,4416
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aiagents4pharma/talk2knowledgegraphs/tests/test_tools_graphrag_reasoning.py,sha256=aOKHTber2Cg3mjNjfIa6RZU7XdFj5C2ps1YEUXw76CI,10650
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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_tools_subgraph_summarization.py,sha256=oBqfspXXOxH04OQuPb8BCW0liIQTGKXtaPNSrPpQtFc,7597
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aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py,sha256=uYFoE_6zeU10_1mLLAHUr5c4S2XZMSc0Q_860o-KWEw,1517
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aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_huggingface.py,sha256=hzX84pheZdEsTtikF2KtBFiH44_xPjYXxLA6p4Ax1CY,1623
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aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py,sha256=G13Diw7cA5TGINUNO1CDnN4rM6KbepxRXNjuzY578DI,1611
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aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py,sha256=K1Y6QM0MDP1IrAdcWkigl8R-O-i-lsL4NCyOrWewhdM,1246
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aiagents4pharma/talk2knowledgegraphs/tools/multimodal_subgraph_extraction.py,sha256=Qjl8hXG8Gv5jQ4pBX8me0pGGakqRZmcDfTGgdEHD9pc,15394
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