tooluniverse 1.0.8__tar.gz → 1.0.9__tar.gz

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  1. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/PKG-INFO +2 -1
  2. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/pyproject.toml +6 -5
  3. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/__init__.py +8 -0
  4. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/admetai_tool.py +8 -1
  5. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/output_summarizer.py +87 -33
  6. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_tool.py +2 -2
  7. tooluniverse-1.0.9/src/tooluniverse/data/adverse_event_tools.json +107 -0
  8. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/agentic_tools.json +81 -162
  9. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/compose_tools.json +0 -54
  10. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/drug_discovery_agents.json +10 -20
  11. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/literature_search_tools.json +15 -35
  12. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/monarch_tools.json +1 -2
  13. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/opentarget_tools.json +8 -16
  14. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/output_summarization_tools.json +23 -20
  15. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/bioinformatics_core_tools.json +2 -2
  16. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/cheminformatics_tools.json +1 -1
  17. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/genomics_tools.json +1 -1
  18. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/single_cell_tools.json +1 -1
  19. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/structural_biology_tools.json +1 -1
  20. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/tool_composition_tools.json +2 -4
  21. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/execute_function.py +39 -1
  22. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/logging_config.py +64 -2
  23. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/molecule_2d_tool.py +9 -3
  24. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/molecule_3d_tool.py +9 -3
  25. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/output_hook.py +217 -150
  26. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/smcp.py +8 -1
  27. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/smcp_server.py +89 -199
  28. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/tools/__init__.py +1 -3
  29. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse.egg-info/PKG-INFO +2 -1
  30. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse.egg-info/SOURCES.txt +4 -2
  31. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse.egg-info/entry_points.txt +0 -3
  32. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse.egg-info/requires.txt +1 -0
  33. tooluniverse-1.0.9/tests/test_cache_manager.py +87 -0
  34. tooluniverse-1.0.9/tests/test_stdio_hooks.py +151 -0
  35. tooluniverse-1.0.9/tests/test_tooluniverse_cache_integration.py +203 -0
  36. tooluniverse-1.0.8/src/tooluniverse/data/adverse_event_tools.json +0 -108
  37. tooluniverse-1.0.8/src/tooluniverse/tools/MultiAgentLiteratureSearch.py +0 -59
  38. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/LICENSE +0 -0
  39. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/README.md +0 -0
  40. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/setup.cfg +0 -0
  41. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/agentic_tool.py +0 -0
  42. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/alphafold_tool.py +0 -0
  43. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/arxiv_tool.py +0 -0
  44. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/base_tool.py +0 -0
  45. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/biogrid_tool.py +0 -0
  46. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/biorxiv_tool.py +0 -0
  47. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/boltz_tool.py +0 -0
  48. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/build_optimizer.py +0 -0
  49. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/cache/__init__.py +0 -0
  50. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/cache/memory_cache.py +0 -0
  51. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/cache/result_cache_manager.py +0 -0
  52. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/cache/sqlite_backend.py +0 -0
  53. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/cellosaurus_tool.py +0 -0
  54. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/chem_tool.py +0 -0
  55. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/clinvar_tool.py +0 -0
  56. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/__init__.py +0 -0
  57. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/biomarker_discovery.py +0 -0
  58. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/comprehensive_drug_discovery.py +0 -0
  59. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/drug_safety_analyzer.py +0 -0
  60. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/enhanced_multi_agent_literature_search.py +0 -0
  61. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/literature_tool.py +0 -0
  62. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/multi_agent_literature_search.py +0 -0
  63. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/tool_description_optimizer.py +0 -0
  64. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/tool_discover.py +0 -0
  65. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/tool_graph_composer.py +0 -0
  66. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/tool_graph_generation.py +0 -0
  67. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/compose_scripts/tool_metadata_generator.py +0 -0
  68. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/core_tool.py +0 -0
  69. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/crossref_tool.py +0 -0
  70. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/ctg_tool.py +0 -0
  71. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/custom_tool.py +0 -0
  72. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/dailymed_tool.py +0 -0
  73. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/__init__.py +0 -0
  74. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/admetai_tools.json +0 -0
  75. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/alphafold_tools.json +0 -0
  76. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/arxiv_tools.json +0 -0
  77. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/biorxiv_tools.json +0 -0
  78. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/boltz_tools.json +0 -0
  79. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/cellosaurus_tools.json +0 -0
  80. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/chembl_tools.json +0 -0
  81. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/clinicaltrials_gov_tools.json +0 -0
  82. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/core_tools.json +0 -0
  83. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/crossref_tools.json +0 -0
  84. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/dailymed_tools.json +0 -0
  85. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/dataset_tools.json +0 -0
  86. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/dblp_tools.json +0 -0
  87. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/disease_target_score_tools.json +0 -0
  88. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/doaj_tools.json +0 -0
  89. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/efo_tools.json +0 -0
  90. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/embedding_tools.json +0 -0
  91. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/enrichr_tools.json +0 -0
  92. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/europe_pmc_tools.json +0 -0
  93. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/expert_feedback_tools.json +0 -0
  94. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/fatcat_tools.json +0 -0
  95. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/fda_drug_adverse_event_tools.json +0 -0
  96. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/fda_drug_labeling_tools.json +0 -0
  97. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py +0 -0
  98. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/finder_tools.json +0 -0
  99. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/gene_ontology_tools.json +0 -0
  100. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/genomics_tools.json +0 -0
  101. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/geo_tools.json +0 -0
  102. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/gwas_tools.json +0 -0
  103. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/hal_tools.json +0 -0
  104. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/hpa_tools.json +0 -0
  105. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/humanbase_tools.json +0 -0
  106. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/idmap_tools.json +0 -0
  107. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/markitdown_tools.json +0 -0
  108. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/mcp_client_tools_example.json +0 -0
  109. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/mcpautoloadertool_defaults.json +0 -0
  110. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/medlineplus_tools.json +0 -0
  111. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/medrxiv_tools.json +0 -0
  112. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/molecule_2d_tools.json +0 -0
  113. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/molecule_3d_tools.json +0 -0
  114. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/odphp_tools.json +0 -0
  115. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/openaire_tools.json +0 -0
  116. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/openalex_tools.json +0 -0
  117. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/osf_preprints_tools.json +0 -0
  118. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/categorized_tools.txt +0 -0
  119. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/earth_sciences_tools.json +0 -0
  120. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/image_processing_tools.json +0 -0
  121. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/machine_learning_tools.json +0 -0
  122. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/neuroscience_tools.json +0 -0
  123. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/original_tools.txt +0 -0
  124. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/physics_astronomy_tools.json +0 -0
  125. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/scientific_computing_tools.json +0 -0
  126. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/packages/visualization_tools.json +0 -0
  127. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/pmc_tools.json +0 -0
  128. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/ppi_tools.json +0 -0
  129. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/protein_structure_3d_tools.json +0 -0
  130. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/pubchem_tools.json +0 -0
  131. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/pubmed_tools.json +0 -0
  132. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/pubtator_tools.json +0 -0
  133. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/rcsb_pdb_tools.json +0 -0
  134. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/reactome_tools.json +0 -0
  135. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/semantic_scholar_tools.json +0 -0
  136. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/special_tools.json +0 -0
  137. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/toolfinderkeyword_defaults.json +0 -0
  138. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/txagent_client_tools.json +0 -0
  139. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/unified_guideline_tools.json +0 -0
  140. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/uniprot_tools.json +0 -0
  141. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/unpaywall_tools.json +0 -0
  142. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/url_fetch_tools.json +0 -0
  143. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/uspto_downloader_tools.json +0 -0
  144. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/uspto_tools.json +0 -0
  145. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/wikidata_sparql_tools.json +0 -0
  146. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/xml_tools.json +0 -0
  147. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/data/zenodo_tools.json +0 -0
  148. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/dataset_tool.py +0 -0
  149. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/dblp_tool.py +0 -0
  150. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/dbsnp_tool.py +0 -0
  151. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/default_config.py +0 -0
  152. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/doaj_tool.py +0 -0
  153. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/doctor.py +0 -0
  154. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/efo_tool.py +0 -0
  155. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/embedding_database.py +0 -0
  156. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/embedding_sync.py +0 -0
  157. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/enrichr_tool.py +0 -0
  158. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/ensembl_tool.py +0 -0
  159. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/europe_pmc_tool.py +0 -0
  160. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/exceptions.py +0 -0
  161. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/extended_hooks.py +0 -0
  162. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/fatcat_tool.py +0 -0
  163. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/gene_ontology_tool.py +0 -0
  164. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/generate_tools.py +0 -0
  165. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/genomics_gene_search_tool.py +0 -0
  166. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/geo_tool.py +0 -0
  167. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/gnomad_tool.py +0 -0
  168. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/graphql_tool.py +0 -0
  169. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/gwas_tool.py +0 -0
  170. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/hal_tool.py +0 -0
  171. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/hpa_tool.py +0 -0
  172. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/humanbase_tool.py +0 -0
  173. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/llm_clients.py +0 -0
  174. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/markitdown_tool.py +0 -0
  175. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/mcp_client_tool.py +0 -0
  176. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/mcp_integration.py +0 -0
  177. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/mcp_tool_registry.py +0 -0
  178. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/medlineplus_tool.py +0 -0
  179. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/medrxiv_tool.py +0 -0
  180. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/memory_manager.py +0 -0
  181. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/odphp_tool.py +0 -0
  182. {tooluniverse-1.0.8 → tooluniverse-1.0.9}/src/tooluniverse/openaire_tool.py +0 -0
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@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: tooluniverse
3
- Version: 1.0.8
3
+ Version: 1.0.9
4
4
  Summary: A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows.
5
5
  Author-email: Shanghua Gao <shanghuagao@gmail.com>
6
6
  Project-URL: Homepage, https://github.com/mims-harvard/ToolUniverse
@@ -29,6 +29,7 @@ Requires-Dist: sentence-transformers>=5.1.0
29
29
  Requires-Dist: fitz>=0.0.1.dev2
30
30
  Requires-Dist: pandas>=2.2.3
31
31
  Requires-Dist: admet-ai>=1.2.0
32
+ Requires-Dist: setuptools>=70.0.0
32
33
  Requires-Dist: pdfplumber>=0.11.0
33
34
  Requires-Dist: playwright>=1.55.0
34
35
  Requires-Dist: faiss-cpu>=1.12.0
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
4
4
 
5
5
  [project]
6
6
  name = "tooluniverse"
7
- version = "1.0.8"
7
+ version = "1.0.9"
8
8
  description = "A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows."
9
9
  authors = [
10
10
  { name = "Shanghua Gao", email = "shanghuagao@gmail.com" }
@@ -32,6 +32,7 @@ dependencies = [
32
32
  "fitz>=0.0.1.dev2",
33
33
  "pandas>=2.2.3",
34
34
  "admet-ai>=1.2.0",
35
+ "setuptools>=70.0.0", # Fix pkg_resources deprecation warnings
35
36
  "pdfplumber>=0.11.0",
36
37
  "playwright>=1.55.0",
37
38
  "faiss-cpu>=1.12.0",
@@ -115,10 +116,10 @@ generate-mcp-tools = "tooluniverse.generate_mcp_tools:run_generate"
115
116
  # Human Expert Feedback System
116
117
  tooluniverse-expert-feedback = "tooluniverse.remote.expert_feedback.human_expert_mcp_tools:main"
117
118
  tooluniverse-expert-feedback-web = "tooluniverse.remote.expert_feedback.start_web_interface:main"
118
- # Literature Search Web UIs
119
- tooluniverse-regular-search = "tooluniverse.web_tools.literature_search_ui.regular_search_app:main"
120
- tooluniverse-agent-search = "tooluniverse.web_tools.literature_search_ui.agent_search_app:main"
121
- tooluniverse-wide-research = "tooluniverse.web_tools.literature_search_ui.simple_app:main"
119
+ # Literature Search Web UIs (Under testing)
120
+ # tooluniverse-regular-search = "tooluniverse.web_tools.literature_search_ui.regular_search_app:main"
121
+ # tooluniverse-agent-search = "tooluniverse.web_tools.literature_search_ui.agent_search_app:main"
122
+ # tooluniverse-wide-research = "tooluniverse.web_tools.literature_search_ui.simple_app:main"
122
123
  # Health Check Tool
123
124
  tooluniverse-doctor = "tooluniverse.doctor:main"
124
125
 
@@ -184,6 +184,14 @@ if not _LIGHT_IMPORT and not LAZY_LOADING_ENABLED:
184
184
  warnings.filterwarnings("ignore", category=RuntimeWarning)
185
185
  warnings.filterwarnings("ignore", category=UserWarning)
186
186
  warnings.filterwarnings("ignore", category=FutureWarning)
187
+ # Suppress specific third-party warnings
188
+ warnings.filterwarnings("ignore", category=UserWarning, module="hyperopt")
189
+ warnings.filterwarnings(
190
+ "ignore", category=DeprecationWarning, module="pkg_resources"
191
+ )
192
+ warnings.filterwarnings(
193
+ "ignore", category=RuntimeWarning, module="importlib._bootstrap"
194
+ )
187
195
 
188
196
  from .restful_tool import MonarchTool, MonarchDiseasesForMultiplePhenoTool
189
197
  from .ctg_tool import ClinicalTrialsSearchTool, ClinicalTrialsDetailsTool
@@ -2,6 +2,7 @@ import numpy
2
2
  from .base_tool import BaseTool
3
3
  from .tool_registry import register_tool
4
4
  import torch
5
+ import warnings
5
6
 
6
7
  # Patch for numpy.VisibleDeprecationWarning for newer numpy versions
7
8
  if not hasattr(numpy, "VisibleDeprecationWarning"):
@@ -21,7 +22,13 @@ def _patched_torch_load(*args, **kwargs):
21
22
 
22
23
  torch.load = _patched_torch_load
23
24
 
24
- from admet_ai import ADMETModel # noqa: E402
25
+ # Suppress admet-ai specific warnings during import
26
+ with warnings.catch_warnings():
27
+ warnings.filterwarnings(
28
+ "ignore", category=DeprecationWarning, module="pkg_resources"
29
+ )
30
+ warnings.filterwarnings("ignore", category=DeprecationWarning, module="admet_ai")
31
+ from admet_ai import ADMETModel # noqa: E402
25
32
 
26
33
 
27
34
  @register_tool("ADMETAITool")
@@ -11,8 +11,12 @@ intelligent, context-aware summarization that focuses on information
11
11
  relevant to the original query.
12
12
  """
13
13
 
14
+ import logging
14
15
  from typing import Dict, Any, List
15
16
 
17
+ # Set up logger for this module
18
+ logger = logging.getLogger("tooluniverse.output_summarizer")
19
+
16
20
 
17
21
  def compose(arguments: Dict[str, Any], tooluniverse, call_tool) -> Dict[str, Any]:
18
22
  """
@@ -30,7 +34,8 @@ def compose(arguments: Dict[str, Any], tooluniverse, call_tool) -> Dict[str, Any
30
34
  - tool_name (str): Name of the tool that generated the output
31
35
  - chunk_size (int, optional): Size of each chunk for processing
32
36
  - focus_areas (str, optional): Areas to focus on in summarization
33
- - max_summary_length (int, optional): Maximum length of final summary
37
+ - max_summary_length (int, optional): Maximum length of final
38
+ summary
34
39
  tooluniverse: ToolUniverse instance for tool execution
35
40
  call_tool: Function to call other tools within the composition
36
41
 
@@ -61,33 +66,53 @@ def compose(arguments: Dict[str, Any], tooluniverse, call_tool) -> Dict[str, Any
61
66
  "original_output": "",
62
67
  }
63
68
 
64
- print(f"🔍 Starting output summarization for {tool_name}")
65
- print(f"📊 Original output length: {len(tool_output)} characters")
69
+ logger.info(f"🔍 Starting output summarization for {tool_name}")
70
+ logger.info(f"📊 Original output length: {len(tool_output)} characters")
71
+
72
+ # Check if text is long enough to warrant summarization
73
+ if len(tool_output) < chunk_size:
74
+ logger.info(
75
+ f"📝 Text is shorter than chunk_size ({chunk_size}), "
76
+ f"no summarization needed"
77
+ )
78
+ return {
79
+ "success": True,
80
+ "original_length": len(tool_output),
81
+ "summary_length": len(tool_output),
82
+ "chunks_processed": 0,
83
+ "summary": tool_output,
84
+ "tool_name": tool_name,
85
+ }
66
86
 
67
87
  # Step 1: Chunk the output
68
88
  chunks = _chunk_output(tool_output, chunk_size)
69
- print(f"📝 Split into {len(chunks)} chunks")
89
+ logger.info(f"📝 Split into {len(chunks)} chunks")
70
90
 
71
91
  # Step 2: Summarize each chunk
72
92
  chunk_summaries = []
73
93
  for i, chunk in enumerate(chunks):
74
- print(f"🤖 Processing chunk {i+1}/{len(chunks)}")
94
+ logger.info(f"🤖 Processing chunk {i+1}/{len(chunks)}")
75
95
  summary = _summarize_chunk(
76
96
  chunk, query_context, tool_name, focus_areas, call_tool
77
97
  )
78
98
  if summary:
79
99
  chunk_summaries.append(summary)
80
- print(f"✅ Chunk {i+1} summarized successfully")
100
+ logger.info(f"✅ Chunk {i+1} summarized successfully")
81
101
  else:
82
- print(f"❌ Chunk {i+1} summarization failed")
102
+ logger.warning(f"❌ Chunk {i+1} summarization failed")
83
103
 
84
104
  # Step 3: Merge summaries (or gracefully fall back)
85
105
  if chunk_summaries:
86
106
  final_summary = _merge_summaries(
87
- chunk_summaries, query_context, tool_name, max_summary_length, call_tool
107
+ chunk_summaries,
108
+ query_context,
109
+ tool_name,
110
+ max_summary_length,
111
+ call_tool,
88
112
  )
89
- print(
90
- f"✅ Summarization completed. Final length: {len(final_summary)} characters"
113
+ logger.info(
114
+ f"✅ Summarization completed. Final length: "
115
+ f"{len(final_summary)} characters"
91
116
  )
92
117
  return {
93
118
  "success": True,
@@ -98,12 +123,17 @@ def compose(arguments: Dict[str, Any], tooluniverse, call_tool) -> Dict[str, Any
98
123
  "tool_name": tool_name,
99
124
  }
100
125
  else:
101
- # Treat as a non-fatal failure so upstream falls back to original output
102
- print("❌ No chunk summaries were generated. This usually indicates:")
103
- print(" 1. ToolOutputSummarizer tool is not available")
104
- print(" 2. The output_summarization tools are not loaded")
105
- print(" 3. There was an error in the summarization process")
106
- print(" Please check that the SMCP server is started with hooks enabled.")
126
+ # Treat as a non-fatal failure so upstream falls back to original
127
+ # output
128
+ logger.warning(
129
+ " No chunk summaries were generated. This usually indicates:"
130
+ )
131
+ logger.warning(" 1. ToolOutputSummarizer tool is not available")
132
+ logger.warning(" 2. The output_summarization tools are not loaded")
133
+ logger.warning(" 3. There was an error in the summarization process")
134
+ logger.warning(
135
+ " Please check that the SMCP server is started with hooks " "enabled."
136
+ )
107
137
  return {
108
138
  "success": False,
109
139
  "error": "No chunk summaries generated",
@@ -115,13 +145,18 @@ def compose(arguments: Dict[str, Any], tooluniverse, call_tool) -> Dict[str, Any
115
145
 
116
146
  except Exception as e:
117
147
  error_msg = f"Error in output summarization: {str(e)}"
118
- print(f"❌ {error_msg}")
119
- return {"success": False, "error": error_msg, "original_output": tool_output}
148
+ logger.error(f"❌ {error_msg}")
149
+ return {
150
+ "success": False,
151
+ "error": error_msg,
152
+ "original_output": tool_output,
153
+ }
120
154
 
121
155
 
122
156
  def _chunk_output(text: str, chunk_size: int) -> List[str]:
123
157
  """
124
- Split text into chunks of specified size with intelligent boundary detection.
158
+ Split text into chunks of specified size with intelligent boundary
159
+ detection.
125
160
 
126
161
  This function attempts to break text at natural boundaries (sentences)
127
162
  to maintain coherence within chunks while respecting the size limit.
@@ -177,8 +212,9 @@ def _summarize_chunk(
177
212
  str: Summarized chunk text, or empty string if summarization fails
178
213
  """
179
214
  try:
180
- print(
181
- f"🔍 Attempting to call ToolOutputSummarizer with chunk length: {len(chunk)}"
215
+ logger.debug(
216
+ f"🔍 Attempting to call ToolOutputSummarizer with chunk length: "
217
+ f"{len(chunk)}"
182
218
  )
183
219
  result = call_tool(
184
220
  "ToolOutputSummarizer",
@@ -191,32 +227,50 @@ def _summarize_chunk(
191
227
  },
192
228
  )
193
229
 
194
- print(
195
- f"🔍 ToolOutputSummarizer returned: {type(result)} - {str(result)[:100]}..."
230
+ logger.debug(
231
+ f"🔍 ToolOutputSummarizer returned: {type(result)} - "
232
+ f"{str(result)[:100]}..."
196
233
  )
197
234
 
198
235
  # Handle different result formats
199
- if isinstance(result, dict) and result.get("success"):
200
- return result.get("result", "")
236
+ if isinstance(result, dict):
237
+ if result.get("success"):
238
+ return result.get("result", "")
239
+ elif "result" in result and isinstance(result["result"], str):
240
+ # ComposeTool._call_tool returns {'result': 'content'} format
241
+ return result["result"]
242
+ elif "error" in result and isinstance(result["error"], str):
243
+ # Backward compatibility: ComposeTool._call_tool used to put
244
+ # string results in error field. This workaround handles both
245
+ # old and new behavior
246
+ return result["error"]
247
+ else:
248
+ logger.warning(f"⚠️ ToolOutputSummarizer returned error: {result}")
249
+ return ""
201
250
  elif isinstance(result, str):
251
+ # When return_metadata=False and successful, AgenticTool returns
252
+ # the string directly
202
253
  return result
203
254
  else:
204
- print(
205
- f"⚠️ ToolOutputSummarizer returned unexpected result format: {type(result)}"
255
+ logger.warning(
256
+ f"⚠️ ToolOutputSummarizer returned unexpected result format: "
257
+ f"{type(result)}"
206
258
  )
207
259
  return ""
208
260
 
209
261
  except Exception as e:
210
262
  error_msg = str(e)
211
- print(f"⚠️ Error summarizing chunk: {error_msg}")
263
+ logger.warning(f"⚠️ Error summarizing chunk: {error_msg}")
212
264
 
213
265
  # Check if the error is due to missing tool
214
266
  if "not found" in error_msg.lower() or "ToolOutputSummarizer" in error_msg:
215
- print(
216
- "❌ ToolOutputSummarizer tool is not available. This indicates the output_summarization tools are not loaded."
267
+ logger.warning(
268
+ "❌ ToolOutputSummarizer tool is not available. This indicates "
269
+ "the output_summarization tools are not loaded."
217
270
  )
218
- print(
219
- " Please ensure the SMCP server is started with hooks enabled and the output_summarization category is loaded."
271
+ logger.warning(
272
+ " Please ensure the SMCP server is started with hooks "
273
+ "enabled and the output_summarization category is loaded."
220
274
  )
221
275
 
222
276
  return ""
@@ -281,5 +335,5 @@ def _merge_summaries(
281
335
  return combined_summaries
282
336
 
283
337
  except Exception as e:
284
- print(f"⚠️ Error merging summaries: {str(e)}")
338
+ logger.warning(f"⚠️ Error merging summaries: {str(e)}")
285
339
  return combined_summaries
@@ -447,8 +447,8 @@ class ComposeTool(BaseTool):
447
447
  else:
448
448
  return {"result": parsed_result}
449
449
  except (json.JSONDecodeError, TypeError):
450
- # If it's not JSON, treat as error message
451
- return {"error": result}
450
+ # If it's not JSON, treat as normal string result
451
+ return {"result": result}
452
452
  elif isinstance(result, dict):
453
453
  return result
454
454
  else:
@@ -0,0 +1,107 @@
1
+ [
2
+ {
3
+ "type": "AgenticTool",
4
+ "name": "AdverseEventPredictionQuestionGenerator",
5
+ "description": "Generates a set of personalized adverse‐event prediction questions for a given disease and drug, across multiple patient subgroups.",
6
+ "prompt": "You are a clinical pharmacology and epidemiology expert. Given the following inputs:\n\n- Disease: {disease_name} \n- Drug: {drug_name} \n\nYour task is to generate a hierarchy of personalized adverse-event prediction questions at two levels:\n\n1. **General Safety Check** \n - Identify one broad safety question that asks for as many potential adverse effects as possible beyond the known label, and include only the disease term in the population description.\n\n2. **Population-Specific Extensions** \n - For at least five distinct patient subgroups, build on the general question by adding one or more clinical details unique to that subgroup (e.g., age, sex, comorbidities, organ function, genetic variants, concomitant meds). \n - Each subgroup’s question must: \n - Ask for as many potential adverse effects as possible \n - Include the description of that specific population in the question \n - Specify any relevant time frame and lab or clinical thresholds \n\n**Output structure**: return only a JSON object with two keys:\n\n- `\"general\"`: \n - `\"population\"`: a list containing only the disease term (e.g. `[\"{disease_name}\"]`) \n - `\"question\"`: the broad safety question that asks for as many adverse effects as possible and incorporates the disease description only \n\n- `\"specific\"`: an array of objects, each with: \n - `\"population\"`: a list of terms describing the subgroup (e.g. `[\"72-year-old\", \"female\", \"atrial fibrillation\", \"chronic warfarin\"]`) \n - `\"question\"`: the extended adverse-event prediction question that: \n - asks for as many adverse effects as possible \n - includes the description of that subgroup \n - specifies the time frame and any lab/clinical thresholds \n\n**Example**:\n\n```json\n{\n \"general\": {\n \"population\": [\"mild Alzheimer’s disease\"],\n \"question\": \"In a patient with mild Alzheimer’s disease planning to start Kisunla therapy, what additional safety concerns or adverse effects—beyond those listed in the FDA label—should be monitored?\"\n },\n \"specific\": [\n {\n \"population\": [\"72-year-old\", \"female\", \"atrial fibrillation\", \"chronic warfarin\"],\n \"question\": \"In a 72-year-old female with atrial fibrillation on chronic warfarin therapy, what potential bleeding events or other adverse effects—beyond the FDA label—should be anticipated within 30 days of initiating Kisunla?\"\n },\n {\n \"population\": [\"79-year-old\", \"female\", \">5 cerebral microhemorrhages\", \"baseline MRI\"],\n \"question\": \"In a 79-year-old female with more than five cerebral microhemorrhages on baseline MRI and no prior intracerebral hemorrhage, what non-label adverse intracranial bleeding events or other safety concerns should be discussed before starting Kisunla?\"\n },\n {\n \"population\": [\"70-year-old\", \"male\", \"well-controlled focal epilepsy\", \"seizure-free 5 years\"],\n \"question\": \"In a 70-year-old male with well-controlled focal epilepsy (seizure-free for 5 years), what seizure-related adverse events or other off-label safety issues should be part of counseling within 60 days of Kisunla therapy?\"\n }\n // …at least two more…\n ]\n}\n```",
7
+ "input_arguments": [
8
+ "disease_name",
9
+ "drug_name"
10
+ ],
11
+ "parameter": {
12
+ "type": "object",
13
+ "properties": {
14
+ "disease_name": {
15
+ "type": "string",
16
+ "description": "The name of the disease or condition"
17
+ },
18
+ "drug_name": {
19
+ "type": "string",
20
+ "description": "The name of the drug"
21
+ }
22
+ },
23
+ "required": [
24
+ "disease_name",
25
+ "drug_name"
26
+ ]
27
+ },
28
+ "configs": {
29
+ "api_type": "CHATGPT",
30
+ "model_id": "o3-mini-0131",
31
+ "temperature": 1.0,
32
+ "max_new_tokens": 20480,
33
+ "return_json": true,
34
+ "return_metadata": false
35
+ }
36
+ },
37
+ {
38
+ "type": "AgenticTool",
39
+ "name": "AdverseEventICDMapper",
40
+ "description": "Extracts adverse events from narrative clinical or pharmacovigilance text and maps each event to the most specific ICD-10-CM code.",
41
+ "prompt": "You are a clinically-oriented NLP assistant trained in pharmacovigilance and ICD-10-CM medical coding.\\n\\n**Your task:**\\n1. Read the *Input Text* below.\\n2. Identify every distinct **adverse event** explicitly stated or unambiguously implied.\\n3. For each adverse event, select the **single most specific ICD-10-CM code** that would ordinarily be assigned by a professional coder in the United States.\\n • If several codes are plausible, choose the one that best matches the wording and context (e.g., \"upper-GI haemorrhage\" ⇒ K92.0 rather than the generic K92.2).\\n • If no precise code exists, return the closest valid proxy and append the flag \"≈ (closest match)\".\\n4. Output the results **exactly** in the following JSON array format (no additional keys or commentary):\\n```json\\n[\\n {\\n \"adverse_event\": \"<event term>\",\\n \"icd10cm_code\": \"<code>\",\\n \"code_description\": \"<official ICD-10-CM description>\"\\n }\\n]\\n```\\n5. Preserve the order in which events first appear in the text.\\n6. Do **not** invent adverse events that are absent from the text.\\n7. If the input text contains no adverse events, reply with the empty list `[]`.\\n\\n*Input Text:*\\n{source_text}",
42
+ "input_arguments": [
43
+ "source_text"
44
+ ],
45
+ "parameter": {
46
+ "type": "object",
47
+ "properties": {
48
+ "source_text": {
49
+ "type": "string",
50
+ "description": "Unstructured narrative text that may mention adverse events."
51
+ }
52
+ },
53
+ "required": [
54
+ "source_text"
55
+ ]
56
+ },
57
+ "configs": {
58
+ "api_type": "CHATGPT",
59
+ "model_id": "o4-mini-0416",
60
+ "temperature": 1.0,
61
+ "max_new_tokens": 20480,
62
+ "return_json": false,
63
+ "return_metadata": false
64
+ }
65
+ },
66
+ {
67
+ "type": "AgenticTool",
68
+ "name": "AdverseEventPredictionQuestionGeneratorWithContext",
69
+ "description": "Generates a set of personalized adverse‐event prediction questions for a given disease and drug, incorporating additional context information such as patient medical history, clinical findings, or research data.",
70
+ "prompt": "You are a clinical pharmacology and epidemiology expert. Given the following inputs:\n\n- Disease: {disease_name} \n- Drug: {drug_name}\n- Context Information: {context_information}\n\nYour task is to generate a hierarchy of personalized adverse-event prediction questions at two levels, taking into account the provided context information:\n\n**IMPORTANT RESTRICTIONS:**\n- DO NOT mention ancestry, race, or ethnicity in any questions or population descriptions\n- DO NOT include specific adverse events or side effects in the questions themselves - the questions should ask WHAT adverse effects might occur, not suggest specific ones\n- Questions should be open-ended inquiries about potential adverse effects, not statements about known risks\n\n**Context Integration Guidelines:**\n- Use the context information to inform your understanding of the disease severity, patient characteristics, drug mechanisms, known interactions, or clinical findings\n- Incorporate relevant details from the context to make questions more specific and clinically relevant\n- Consider any special populations, contraindications, or risk factors mentioned in the context\n- Exclude any ancestry-related information from consideration\n\n1. **General Safety Check** \n - Identify one broad safety question that asks for as many potential adverse effects as possible beyond the known label, incorporating relevant context insights and including only the disease term in the population description.\n\n2. **Population-Specific Extensions** \n - For at least five distinct patient subgroups, build on the general question by adding one or more clinical details unique to that subgroup (e.g., age, sex, comorbidities, organ function, genetic variants, concomitant meds). \n - Use context information to identify the most relevant and high-risk subgroups\n - Each subgroup's question must: \n - Ask for as many potential adverse effects as possible \n - Include the description of that specific population in the question \n - Specify any relevant time frame and lab or clinical thresholds\n - Incorporate context-specific risk factors or considerations\n - NOT mention ancestry, race, or ethnicity\n\n**Output structure**: return only a JSON object with three keys:\n\n- `\"context_summary\"`: a brief summary of how the context information influenced the question generation\n\n- `\"general\"`: \n - `\"population\"`: a list containing only the disease term (e.g. `[\"{disease_name}\"]`) \n - `\"question\"`: the broad safety question that asks for as many adverse effects as possible, incorporates the disease description, and reflects context insights \n\n- `\"specific\"`: an array of objects, each with: \n - `\"population\"`: a list of terms describing the subgroup (e.g. `[\"72-year-old\", \"female\", \"atrial fibrillation\", \"chronic warfarin\"]`) \n - `\"question\"`: the extended adverse-event prediction question that: \n - asks for as many adverse effects as possible \n - includes the description of that subgroup \n - specifies the time frame and any lab/clinical thresholds\n - incorporates relevant context considerations\n\n**Example**:\n\n```json\n{\n \"context_summary\": \"Context revealed increased risk factors in elderly patients and potential drug interactions with anticoagulants, leading to enhanced focus on cardiovascular and bleeding-related inquiries.\",\n \"general\": {\n \"population\": [\"mild Alzheimer's disease\"],\n \"question\": \"In a patient with mild Alzheimer's disease planning to start Kisunla therapy, what additional safety concerns or adverse effects—beyond those listed in the FDA label—should be monitored?\"\n },\n \"specific\": [\n {\n \"population\": [\"72-year-old\", \"female\", \"atrial fibrillation\", \"chronic warfarin\"],\n \"question\": \"In a 72-year-old female with atrial fibrillation on chronic warfarin therapy, what potential adverse effects—beyond the FDA label—should be anticipated within 30 days of initiating Kisunla?\"\n },\n {\n \"population\": [\"79-year-old\", \"female\", \">5 cerebral microhemorrhages\", \"baseline MRI\"],\n \"question\": \"In a 79-year-old female with more than five cerebral microhemorrhages on baseline MRI and no prior intracerebral hemorrhage, what adverse events or safety concerns should be discussed before starting Kisunla?\"\n }\n // …at least three more…\n ]\n}\n```",
71
+ "input_arguments": [
72
+ "disease_name",
73
+ "drug_name",
74
+ "context_information"
75
+ ],
76
+ "parameter": {
77
+ "type": "object",
78
+ "properties": {
79
+ "disease_name": {
80
+ "type": "string",
81
+ "description": "The name of the disease or condition"
82
+ },
83
+ "drug_name": {
84
+ "type": "string",
85
+ "description": "The name of the drug"
86
+ },
87
+ "context_information": {
88
+ "type": "string",
89
+ "description": "Additional context information such as patient medical history, clinical findings, research data, or other relevant background information that should inform the adverse event prediction questions"
90
+ }
91
+ },
92
+ "required": [
93
+ "disease_name",
94
+ "drug_name",
95
+ "context_information"
96
+ ]
97
+ },
98
+ "configs": {
99
+ "api_type": "CHATGPT",
100
+ "model_id": "o3-mini-0131",
101
+ "temperature": 1.0,
102
+ "max_new_tokens": 20480,
103
+ "return_json": true,
104
+ "return_metadata": false
105
+ }
106
+ }
107
+ ]