tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

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  1. tooluniverse/__init__.py +56 -10
  2. tooluniverse/admetai_tool.py +8 -4
  3. tooluniverse/agentic_tool.py +40 -4
  4. tooluniverse/arxiv_tool.py +2 -6
  5. tooluniverse/base_tool.py +210 -25
  6. tooluniverse/biogrid_tool.py +118 -0
  7. tooluniverse/biorxiv_tool.py +35 -16
  8. tooluniverse/build_optimizer.py +87 -0
  9. tooluniverse/cache/__init__.py +3 -0
  10. tooluniverse/cache/memory_cache.py +99 -0
  11. tooluniverse/cache/result_cache_manager.py +235 -0
  12. tooluniverse/cache/sqlite_backend.py +257 -0
  13. tooluniverse/cellosaurus_tool.py +1332 -0
  14. tooluniverse/clinvar_tool.py +90 -0
  15. tooluniverse/compose_scripts/enhanced_multi_agent_literature_search.py +310 -0
  16. tooluniverse/compose_scripts/multi_agent_literature_search.py +794 -0
  17. tooluniverse/compose_scripts/tool_graph_generation.py +68 -35
  18. tooluniverse/compose_scripts/tool_metadata_generator.py +205 -105
  19. tooluniverse/compose_tool.py +93 -8
  20. tooluniverse/core_tool.py +46 -44
  21. tooluniverse/crossref_tool.py +89 -4
  22. tooluniverse/custom_tool.py +28 -0
  23. tooluniverse/data/agentic_tools.json +1271 -1179
  24. tooluniverse/data/alphafold_tools.json +356 -105
  25. tooluniverse/data/arxiv_tools.json +85 -81
  26. tooluniverse/data/biorxiv_tools.json +69 -64
  27. tooluniverse/data/cellosaurus_tools.json +260 -0
  28. tooluniverse/data/chembl_tools.json +27 -12
  29. tooluniverse/data/clinicaltrials_gov_tools.json +377 -302
  30. tooluniverse/data/compose_tools.json +123 -16
  31. tooluniverse/data/core_tools.json +104 -99
  32. tooluniverse/data/crossref_tools.json +131 -63
  33. tooluniverse/data/dailymed_tools.json +17 -3
  34. tooluniverse/data/dataset_tools.json +1031 -588
  35. tooluniverse/data/dblp_tools.json +135 -64
  36. tooluniverse/data/disease_target_score_tools.json +20 -10
  37. tooluniverse/data/doaj_tools.json +131 -87
  38. tooluniverse/data/drug_discovery_agents.json +292 -0
  39. tooluniverse/data/embedding_tools.json +362 -299
  40. tooluniverse/data/enrichr_tools.json +34 -27
  41. tooluniverse/data/europe_pmc_tools.json +107 -16
  42. tooluniverse/data/fatcat_tools.json +71 -66
  43. tooluniverse/data/fda_drug_adverse_event_tools.json +1061 -445
  44. tooluniverse/data/fda_drug_labeling_tools.json +6858 -6901
  45. tooluniverse/data/finder_tools.json +32 -37
  46. tooluniverse/data/gene_ontology_tools.json +19 -7
  47. tooluniverse/data/genomics_tools.json +174 -0
  48. tooluniverse/data/geo_tools.json +86 -0
  49. tooluniverse/data/gwas_tools.json +1720 -959
  50. tooluniverse/data/hal_tools.json +69 -64
  51. tooluniverse/data/hpa_tools.json +53 -14
  52. tooluniverse/data/humanbase_tools.json +51 -43
  53. tooluniverse/data/idmap_tools.json +76 -70
  54. tooluniverse/data/literature_search_tools.json +306 -0
  55. tooluniverse/data/markitdown_tools.json +51 -0
  56. tooluniverse/data/mcp_client_tools_example.json +122 -107
  57. tooluniverse/data/medlineplus_tools.json +50 -10
  58. tooluniverse/data/medrxiv_tools.json +69 -64
  59. tooluniverse/data/molecule_2d_tools.json +134 -0
  60. tooluniverse/data/molecule_3d_tools.json +164 -0
  61. tooluniverse/data/monarch_tools.json +112 -110
  62. tooluniverse/data/odphp_tools.json +389 -119
  63. tooluniverse/data/openaire_tools.json +89 -79
  64. tooluniverse/data/openalex_tools.json +96 -31
  65. tooluniverse/data/opentarget_tools.json +1457 -1372
  66. tooluniverse/data/osf_preprints_tools.json +77 -73
  67. tooluniverse/data/packages/bioinformatics_core_tools.json +40 -10
  68. tooluniverse/data/packages/cheminformatics_tools.json +20 -5
  69. tooluniverse/data/packages/genomics_tools.json +36 -9
  70. tooluniverse/data/packages/machine_learning_tools.json +36 -9
  71. tooluniverse/data/packages/scientific_computing_tools.json +20 -5
  72. tooluniverse/data/packages/single_cell_tools.json +20 -5
  73. tooluniverse/data/packages/structural_biology_tools.json +16 -4
  74. tooluniverse/data/packages/visualization_tools.json +20 -5
  75. tooluniverse/data/pmc_tools.json +108 -103
  76. tooluniverse/data/ppi_tools.json +139 -0
  77. tooluniverse/data/protein_structure_3d_tools.json +138 -0
  78. tooluniverse/data/pubchem_tools.json +37 -12
  79. tooluniverse/data/pubmed_tools.json +124 -58
  80. tooluniverse/data/pubtator_tools.json +68 -60
  81. tooluniverse/data/rcsb_pdb_tools.json +1532 -1221
  82. tooluniverse/data/semantic_scholar_tools.json +54 -22
  83. tooluniverse/data/special_tools.json +8 -6
  84. tooluniverse/data/tool_composition_tools.json +112 -82
  85. tooluniverse/data/unified_guideline_tools.json +909 -0
  86. tooluniverse/data/url_fetch_tools.json +102 -82
  87. tooluniverse/data/uspto_tools.json +49 -30
  88. tooluniverse/data/wikidata_sparql_tools.json +42 -39
  89. tooluniverse/data/xml_tools.json +3274 -3113
  90. tooluniverse/data/zenodo_tools.json +83 -76
  91. tooluniverse/dblp_tool.py +76 -6
  92. tooluniverse/dbsnp_tool.py +71 -0
  93. tooluniverse/default_config.py +19 -0
  94. tooluniverse/doaj_tool.py +76 -17
  95. tooluniverse/doctor.py +48 -0
  96. tooluniverse/ensembl_tool.py +61 -0
  97. tooluniverse/europe_pmc_tool.py +132 -17
  98. tooluniverse/exceptions.py +170 -0
  99. tooluniverse/execute_function.py +930 -387
  100. tooluniverse/fatcat_tool.py +0 -1
  101. tooluniverse/generate_tools.py +481 -0
  102. tooluniverse/genomics_gene_search_tool.py +56 -0
  103. tooluniverse/geo_tool.py +116 -0
  104. tooluniverse/gnomad_tool.py +63 -0
  105. tooluniverse/hal_tool.py +1 -1
  106. tooluniverse/llm_clients.py +101 -124
  107. tooluniverse/markitdown_tool.py +159 -0
  108. tooluniverse/mcp_client_tool.py +10 -5
  109. tooluniverse/mcp_tool_registry.py +4 -1
  110. tooluniverse/medrxiv_tool.py +32 -13
  111. tooluniverse/memory_manager.py +166 -0
  112. tooluniverse/molecule_2d_tool.py +274 -0
  113. tooluniverse/molecule_3d_tool.py +441 -0
  114. tooluniverse/odphp_tool.py +49 -14
  115. tooluniverse/openaire_tool.py +5 -20
  116. tooluniverse/openalex_tool.py +34 -0
  117. tooluniverse/osf_preprints_tool.py +1 -1
  118. tooluniverse/pmc_tool.py +54 -56
  119. tooluniverse/protein_structure_3d_tool.py +295 -0
  120. tooluniverse/pubmed_tool.py +69 -6
  121. tooluniverse/remote/boltz/boltz_mcp_server.py +3 -1
  122. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +3 -1
  123. tooluniverse/semantic_scholar_tool.py +40 -10
  124. tooluniverse/smcp.py +149 -213
  125. tooluniverse/smcp_server.py +97 -55
  126. tooluniverse/string_tool.py +112 -0
  127. tooluniverse/tool_registry.py +35 -3
  128. tooluniverse/tools/ADMETAI_predict_BBB_penetrance.py +46 -0
  129. tooluniverse/tools/ADMETAI_predict_CYP_interactions.py +46 -0
  130. tooluniverse/tools/ADMETAI_predict_bioavailability.py +46 -0
  131. tooluniverse/tools/ADMETAI_predict_clearance_distribution.py +49 -0
  132. tooluniverse/tools/ADMETAI_predict_nuclear_receptor_activity.py +49 -0
  133. tooluniverse/tools/ADMETAI_predict_physicochemical_properties.py +49 -0
  134. tooluniverse/tools/ADMETAI_predict_solubility_lipophilicity_hydration.py +49 -0
  135. tooluniverse/tools/ADMETAI_predict_stress_response.py +46 -0
  136. tooluniverse/tools/ADMETAI_predict_toxicity.py +46 -0
  137. tooluniverse/tools/ADMETAnalyzerAgent.py +59 -0
  138. tooluniverse/tools/AdvancedCodeQualityAnalyzer.py +63 -0
  139. tooluniverse/tools/AdverseEventICDMapper.py +46 -0
  140. tooluniverse/tools/AdverseEventPredictionQuestionGenerator.py +52 -0
  141. tooluniverse/tools/AdverseEventPredictionQuestionGeneratorWithContext.py +59 -0
  142. tooluniverse/tools/ArXiv_search_papers.py +63 -0
  143. tooluniverse/tools/ArgumentDescriptionOptimizer.py +55 -0
  144. tooluniverse/tools/BioRxiv_search_preprints.py +52 -0
  145. tooluniverse/tools/BiomarkerDiscoveryWorkflow.py +55 -0
  146. tooluniverse/tools/CMA_Guidelines_Search.py +52 -0
  147. tooluniverse/tools/CORE_search_papers.py +67 -0
  148. tooluniverse/tools/CallAgent.py +46 -0
  149. tooluniverse/tools/ChEMBL_search_similar_molecules.py +59 -0
  150. tooluniverse/tools/ClinVar_search_variants.py +52 -0
  151. tooluniverse/tools/ClinicalTrialDesignAgent.py +63 -0
  152. tooluniverse/tools/CodeOptimizer.py +55 -0
  153. tooluniverse/tools/CodeQualityAnalyzer.py +71 -0
  154. tooluniverse/tools/CompoundDiscoveryAgent.py +59 -0
  155. tooluniverse/tools/ComprehensiveDrugDiscoveryPipeline.py +49 -0
  156. tooluniverse/tools/Crossref_search_works.py +55 -0
  157. tooluniverse/tools/DBLP_search_publications.py +52 -0
  158. tooluniverse/tools/DOAJ_search_articles.py +55 -0
  159. tooluniverse/tools/DailyMed_get_spl_by_setid.py +52 -0
  160. tooluniverse/tools/DailyMed_search_spls.py +79 -0
  161. tooluniverse/tools/DataAnalysisValidityReviewer.py +49 -0
  162. tooluniverse/tools/DescriptionAnalyzer.py +55 -0
  163. tooluniverse/tools/DescriptionQualityEvaluator.py +59 -0
  164. tooluniverse/tools/DiseaseAnalyzerAgent.py +52 -0
  165. tooluniverse/tools/DomainExpertValidator.py +63 -0
  166. tooluniverse/tools/DrugInteractionAnalyzerAgent.py +52 -0
  167. tooluniverse/tools/DrugOptimizationAgent.py +63 -0
  168. tooluniverse/tools/DrugSafetyAnalyzer.py +59 -0
  169. tooluniverse/tools/Ensembl_lookup_gene_by_symbol.py +52 -0
  170. tooluniverse/tools/EthicalComplianceReviewer.py +49 -0
  171. tooluniverse/tools/EuropePMC_Guidelines_Search.py +52 -0
  172. tooluniverse/tools/EuropePMC_search_articles.py +52 -0
  173. tooluniverse/tools/ExperimentalDesignScorer.py +55 -0
  174. tooluniverse/tools/FAERS_count_additive_administration_routes.py +52 -0
  175. tooluniverse/tools/FAERS_count_additive_adverse_reactions.py +71 -0
  176. tooluniverse/tools/FAERS_count_additive_event_reports_by_country.py +63 -0
  177. tooluniverse/tools/FAERS_count_additive_reaction_outcomes.py +63 -0
  178. tooluniverse/tools/FAERS_count_additive_reports_by_reporter_country.py +63 -0
  179. tooluniverse/tools/FAERS_count_additive_seriousness_classification.py +63 -0
  180. tooluniverse/tools/FAERS_count_country_by_drug_event.py +63 -0
  181. tooluniverse/tools/FAERS_count_death_related_by_drug.py +49 -0
  182. tooluniverse/tools/FAERS_count_drug_routes_by_event.py +52 -0
  183. tooluniverse/tools/FAERS_count_drugs_by_drug_event.py +63 -0
  184. tooluniverse/tools/FAERS_count_outcomes_by_drug_event.py +63 -0
  185. tooluniverse/tools/FAERS_count_patient_age_distribution.py +49 -0
  186. tooluniverse/tools/FAERS_count_reactions_by_drug_event.py +71 -0
  187. tooluniverse/tools/FAERS_count_reportercountry_by_drug_event.py +63 -0
  188. tooluniverse/tools/FAERS_count_seriousness_by_drug_event.py +63 -0
  189. tooluniverse/tools/FDA_get_abuse_dependence_info_by_drug_name.py +55 -0
  190. tooluniverse/tools/FDA_get_abuse_info_by_drug_name.py +55 -0
  191. tooluniverse/tools/FDA_get_accessories_info_by_drug_name.py +55 -0
  192. tooluniverse/tools/FDA_get_active_ingredient_info_by_drug_name.py +55 -0
  193. tooluniverse/tools/FDA_get_adverse_reactions_by_drug_name.py +55 -0
  194. tooluniverse/tools/FDA_get_alarms_by_drug_name.py +55 -0
  195. tooluniverse/tools/FDA_get_animal_pharmacology_info_by_drug_name.py +55 -0
  196. tooluniverse/tools/FDA_get_assembly_installation_info_by_drug_name.py +55 -0
  197. tooluniverse/tools/FDA_get_boxed_warning_info_by_drug_name.py +55 -0
  198. tooluniverse/tools/FDA_get_brand_name_generic_name.py +52 -0
  199. tooluniverse/tools/FDA_get_calibration_instructions_by_drug_name.py +55 -0
  200. tooluniverse/tools/FDA_get_carcinogenic_mutagenic_fertility_by_drug_name.py +55 -0
  201. tooluniverse/tools/FDA_get_child_safety_info_by_drug_name.py +55 -0
  202. tooluniverse/tools/FDA_get_clinical_pharmacology_by_drug_name.py +55 -0
  203. tooluniverse/tools/FDA_get_clinical_studies_info_by_drug_name.py +55 -0
  204. tooluniverse/tools/FDA_get_contact_for_questions_info_by_drug_name.py +55 -0
  205. tooluniverse/tools/FDA_get_contraindications_by_drug_name.py +55 -0
  206. tooluniverse/tools/FDA_get_controlled_substance_DEA_schedule_info_by_drug_name.py +55 -0
  207. tooluniverse/tools/FDA_get_dear_health_care_provider_letter_info_by_drug_name.py +55 -0
  208. tooluniverse/tools/FDA_get_dependence_info_by_drug_name.py +55 -0
  209. tooluniverse/tools/FDA_get_disposal_info_by_drug_name.py +55 -0
  210. tooluniverse/tools/FDA_get_do_not_use_info_by_drug_name.py +55 -0
  211. tooluniverse/tools/FDA_get_document_id_by_drug_name.py +55 -0
  212. tooluniverse/tools/FDA_get_dosage_and_storage_information_by_drug_name.py +55 -0
  213. tooluniverse/tools/FDA_get_dosage_forms_and_strengths_by_drug_name.py +55 -0
  214. tooluniverse/tools/FDA_get_drug_generic_name.py +46 -0
  215. tooluniverse/tools/FDA_get_drug_interactions_by_drug_name.py +55 -0
  216. tooluniverse/tools/FDA_get_drug_name_by_SPL_ID.py +55 -0
  217. tooluniverse/tools/FDA_get_drug_name_by_adverse_reaction.py +59 -0
  218. tooluniverse/tools/FDA_get_drug_name_by_calibration_instructions.py +59 -0
  219. tooluniverse/tools/FDA_get_drug_name_by_dependence_info.py +59 -0
  220. tooluniverse/tools/FDA_get_drug_name_by_document_id.py +55 -0
  221. tooluniverse/tools/FDA_get_drug_name_by_dosage_info.py +55 -0
  222. tooluniverse/tools/FDA_get_drug_name_by_environmental_warning.py +59 -0
  223. tooluniverse/tools/FDA_get_drug_name_by_inactive_ingredient.py +59 -0
  224. tooluniverse/tools/FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation.py +55 -0
  225. tooluniverse/tools/FDA_get_drug_name_by_labor_and_delivery_info.py +59 -0
  226. tooluniverse/tools/FDA_get_drug_name_by_microbiology.py +59 -0
  227. tooluniverse/tools/FDA_get_drug_name_by_other_safety_info.py +55 -0
  228. tooluniverse/tools/FDA_get_drug_name_by_pharmacodynamics.py +59 -0
  229. tooluniverse/tools/FDA_get_drug_name_by_pharmacogenomics.py +59 -0
  230. tooluniverse/tools/FDA_get_drug_name_by_precautions.py +55 -0
  231. tooluniverse/tools/FDA_get_drug_name_by_pregnancy_or_breastfeeding_info.py +59 -0
  232. tooluniverse/tools/FDA_get_drug_name_by_principal_display_panel.py +59 -0
  233. tooluniverse/tools/FDA_get_drug_name_by_reference.py +55 -0
  234. tooluniverse/tools/FDA_get_drug_name_by_set_id.py +55 -0
  235. tooluniverse/tools/FDA_get_drug_name_by_stop_use_info.py +55 -0
  236. tooluniverse/tools/FDA_get_drug_name_by_storage_and_handling_info.py +55 -0
  237. tooluniverse/tools/FDA_get_drug_name_by_warnings.py +55 -0
  238. tooluniverse/tools/FDA_get_drug_name_from_patient_package_insert.py +59 -0
  239. tooluniverse/tools/FDA_get_drug_names_by_abuse_dependence_info.py +55 -0
  240. tooluniverse/tools/FDA_get_drug_names_by_abuse_info.py +63 -0
  241. tooluniverse/tools/FDA_get_drug_names_by_accessories.py +63 -0
  242. tooluniverse/tools/FDA_get_drug_names_by_active_ingredient.py +63 -0
  243. tooluniverse/tools/FDA_get_drug_names_by_alarm.py +63 -0
  244. tooluniverse/tools/FDA_get_drug_names_by_animal_pharmacology_info.py +63 -0
  245. tooluniverse/tools/FDA_get_drug_names_by_application_number_NDC_number.py +59 -0
  246. tooluniverse/tools/FDA_get_drug_names_by_assembly_installation_info.py +63 -0
  247. tooluniverse/tools/FDA_get_drug_names_by_boxed_warning.py +63 -0
  248. tooluniverse/tools/FDA_get_drug_names_by_child_safety_info.py +63 -0
  249. tooluniverse/tools/FDA_get_drug_names_by_clinical_pharmacology.py +63 -0
  250. tooluniverse/tools/FDA_get_drug_names_by_clinical_studies.py +63 -0
  251. tooluniverse/tools/FDA_get_drug_names_by_consulting_doctor_pharmacist_info.py +63 -0
  252. tooluniverse/tools/FDA_get_drug_names_by_contraindications.py +63 -0
  253. tooluniverse/tools/FDA_get_drug_names_by_controlled_substance_DEA_schedule.py +63 -0
  254. tooluniverse/tools/FDA_get_drug_names_by_dear_health_care_provider_letter_info.py +63 -0
  255. tooluniverse/tools/FDA_get_drug_names_by_disposal_info.py +63 -0
  256. tooluniverse/tools/FDA_get_drug_names_by_dosage_forms_and_strengths_info.py +63 -0
  257. tooluniverse/tools/FDA_get_drug_names_by_drug_interactions.py +63 -0
  258. tooluniverse/tools/FDA_get_drug_names_by_effective_time.py +63 -0
  259. tooluniverse/tools/FDA_get_drug_names_by_food_safety_warnings.py +63 -0
  260. tooluniverse/tools/FDA_get_drug_names_by_general_precautions.py +63 -0
  261. tooluniverse/tools/FDA_get_drug_names_by_geriatric_use.py +63 -0
  262. tooluniverse/tools/FDA_get_drug_names_by_health_claim.py +63 -0
  263. tooluniverse/tools/FDA_get_drug_names_by_indication.py +55 -0
  264. tooluniverse/tools/FDA_get_drug_names_by_info_for_nursing_mothers.py +63 -0
  265. tooluniverse/tools/FDA_get_drug_names_by_information_for_owners_or_caregivers.py +63 -0
  266. tooluniverse/tools/FDA_get_drug_names_by_ingredient.py +63 -0
  267. tooluniverse/tools/FDA_get_drug_names_by_instructions_for_use.py +63 -0
  268. tooluniverse/tools/FDA_get_drug_names_by_lab_test_interference.py +63 -0
  269. tooluniverse/tools/FDA_get_drug_names_by_lab_tests.py +63 -0
  270. tooluniverse/tools/FDA_get_drug_names_by_mechanism_of_action.py +63 -0
  271. tooluniverse/tools/FDA_get_drug_names_by_medication_guide.py +63 -0
  272. tooluniverse/tools/FDA_get_drug_names_by_nonclinical_toxicology_info.py +63 -0
  273. tooluniverse/tools/FDA_get_drug_names_by_nonteratogenic_effects.py +63 -0
  274. tooluniverse/tools/FDA_get_drug_names_by_overdosage_info.py +63 -0
  275. tooluniverse/tools/FDA_get_drug_names_by_pediatric_use.py +63 -0
  276. tooluniverse/tools/FDA_get_drug_names_by_pharmacokinetics.py +63 -0
  277. tooluniverse/tools/FDA_get_drug_names_by_population_use.py +63 -0
  278. tooluniverse/tools/FDA_get_drug_names_by_pregnancy_effects_info.py +63 -0
  279. tooluniverse/tools/FDA_get_drug_names_by_residue_warning.py +63 -0
  280. tooluniverse/tools/FDA_get_drug_names_by_risk.py +63 -0
  281. tooluniverse/tools/FDA_get_drug_names_by_route.py +63 -0
  282. tooluniverse/tools/FDA_get_drug_names_by_safe_handling_warning.py +63 -0
  283. tooluniverse/tools/FDA_get_drug_names_by_safety_summary.py +63 -0
  284. tooluniverse/tools/FDA_get_drug_names_by_spl_indexing_data_elements.py +63 -0
  285. tooluniverse/tools/FDA_get_drug_names_by_teratogenic_effects.py +63 -0
  286. tooluniverse/tools/FDA_get_drug_names_by_user_safety_warning.py +63 -0
  287. tooluniverse/tools/FDA_get_drug_names_by_warnings_and_cautions.py +63 -0
  288. tooluniverse/tools/FDA_get_drugs_by_carcinogenic_mutagenic_fertility.py +63 -0
  289. tooluniverse/tools/FDA_get_effective_time_by_drug_name.py +55 -0
  290. tooluniverse/tools/FDA_get_environmental_warning_by_drug_name.py +55 -0
  291. tooluniverse/tools/FDA_get_general_precautions_by_drug_name.py +55 -0
  292. tooluniverse/tools/FDA_get_geriatric_use_info_by_drug_name.py +55 -0
  293. tooluniverse/tools/FDA_get_health_claims_by_drug_name.py +55 -0
  294. tooluniverse/tools/FDA_get_inactive_ingredient_info_by_drug_name.py +55 -0
  295. tooluniverse/tools/FDA_get_indications_by_drug_name.py +55 -0
  296. tooluniverse/tools/FDA_get_info_for_nursing_mothers_by_drug_name.py +55 -0
  297. tooluniverse/tools/FDA_get_info_for_patients_by_drug_name.py +55 -0
  298. tooluniverse/tools/FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name.py +55 -0
  299. tooluniverse/tools/FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name.py +55 -0
  300. tooluniverse/tools/FDA_get_information_for_owners_or_caregivers_by_drug_name.py +55 -0
  301. tooluniverse/tools/FDA_get_ingredients_by_drug_name.py +55 -0
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  586. tooluniverse/tools/get_clinical_trial_descriptions.py +52 -0
  587. tooluniverse/tools/get_clinical_trial_eligibility_criteria.py +55 -0
  588. tooluniverse/tools/get_clinical_trial_locations.py +52 -0
  589. tooluniverse/tools/get_clinical_trial_outcome_measures.py +52 -0
  590. tooluniverse/tools/get_clinical_trial_references.py +52 -0
  591. tooluniverse/tools/get_clinical_trial_status_and_dates.py +52 -0
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  596. tooluniverse/tools/get_cryosparc_tools_info.py +46 -0
  597. tooluniverse/tools/get_crystal_growth_conditions_by_pdb_id.py +49 -0
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  599. tooluniverse/tools/get_crystallographic_properties_by_pdb_id.py +49 -0
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  601. tooluniverse/tools/get_cyvcf2_info.py +49 -0
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  610. tooluniverse/tools/get_descriptastorus_info.py +46 -0
  611. tooluniverse/tools/get_diffdock_info.py +46 -0
  612. tooluniverse/tools/get_dscribe_info.py +49 -0
  613. tooluniverse/tools/get_ec_number_by_entity_id.py +46 -0
  614. tooluniverse/tools/get_elephant_info.py +44 -0
  615. tooluniverse/tools/get_em_3d_fitting_and_reconstruction_details.py +49 -0
  616. tooluniverse/tools/get_emdb_ids_by_pdb_id.py +46 -0
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  618. tooluniverse/tools/get_ete3_info.py +44 -0
  619. tooluniverse/tools/get_faiss_info.py +46 -0
  620. tooluniverse/tools/get_fanc_info.py +46 -0
  621. tooluniverse/tools/get_flask_info.py +46 -0
  622. tooluniverse/tools/get_flowio_info.py +46 -0
  623. tooluniverse/tools/get_flowkit_info.py +46 -0
  624. tooluniverse/tools/get_flowutils_info.py +46 -0
  625. tooluniverse/tools/get_freesasa_info.py +44 -0
  626. tooluniverse/tools/get_galpy_info.py +44 -0
  627. tooluniverse/tools/get_gene_name_by_entity_id.py +46 -0
  628. tooluniverse/tools/get_geopandas_info.py +44 -0
  629. tooluniverse/tools/get_gget_info.py +46 -0
  630. tooluniverse/tools/get_googlesearch_python_info.py +46 -0
  631. tooluniverse/tools/get_gseapy_info.py +49 -0
  632. tooluniverse/tools/get_h5py_info.py +46 -0
  633. tooluniverse/tools/get_harmony_pytorch_info.py +46 -0
  634. tooluniverse/tools/get_hmmlearn_info.py +46 -0
  635. tooluniverse/tools/get_holoviews_info.py +44 -0
  636. tooluniverse/tools/get_host_organism_by_pdb_id.py +46 -0
  637. tooluniverse/tools/get_htmd_info.py +44 -0
  638. tooluniverse/tools/get_hyperopt_info.py +49 -0
  639. tooluniverse/tools/get_igraph_info.py +49 -0
  640. tooluniverse/tools/get_imageio_info.py +44 -0
  641. tooluniverse/tools/get_imbalanced_learn_info.py +44 -0
  642. tooluniverse/tools/get_jcvi_info.py +46 -0
  643. tooluniverse/tools/get_joblib_info.py +44 -0
  644. tooluniverse/tools/get_joint_associated_diseases_by_HPO_ID_list.py +55 -0
  645. tooluniverse/tools/get_khmer_info.py +46 -0
  646. tooluniverse/tools/get_kipoiseq_info.py +44 -0
  647. tooluniverse/tools/get_lifelines_info.py +49 -0
  648. tooluniverse/tools/get_ligand_bond_count_by_pdb_id.py +46 -0
  649. tooluniverse/tools/get_ligand_smiles_by_chem_comp_id.py +49 -0
  650. tooluniverse/tools/get_lightgbm_info.py +44 -0
  651. tooluniverse/tools/get_loompy_info.py +46 -0
  652. tooluniverse/tools/get_mageck_info.py +46 -0
  653. tooluniverse/tools/get_matplotlib_info.py +49 -0
  654. tooluniverse/tools/get_mdanalysis_info.py +46 -0
  655. tooluniverse/tools/get_mdtraj_info.py +44 -0
  656. tooluniverse/tools/get_mne_info.py +44 -0
  657. tooluniverse/tools/get_molfeat_info.py +44 -0
  658. tooluniverse/tools/get_molvs_info.py +44 -0
  659. tooluniverse/tools/get_mordred_info.py +44 -0
  660. tooluniverse/tools/get_msprime_info.py +49 -0
  661. tooluniverse/tools/get_mudata_info.py +49 -0
  662. tooluniverse/tools/get_mutation_annotations_by_pdb_id.py +46 -0
  663. tooluniverse/tools/get_neo_info.py +44 -0
  664. tooluniverse/tools/get_netcdf4_info.py +44 -0
  665. tooluniverse/tools/get_networkx_info.py +46 -0
  666. tooluniverse/tools/get_nglview_info.py +44 -0
  667. tooluniverse/tools/get_nilearn_info.py +44 -0
  668. tooluniverse/tools/get_numba_info.py +46 -0
  669. tooluniverse/tools/get_numpy_info.py +46 -0
  670. tooluniverse/tools/get_oligosaccharide_descriptors_by_entity_id.py +49 -0
  671. tooluniverse/tools/get_openbabel_info.py +49 -0
  672. tooluniverse/tools/get_openchem_info.py +46 -0
  673. tooluniverse/tools/get_opencv_info.py +49 -0
  674. tooluniverse/tools/get_openmm_info.py +49 -0
  675. tooluniverse/tools/get_optlang_info.py +46 -0
  676. tooluniverse/tools/get_optuna_info.py +44 -0
  677. tooluniverse/tools/get_palantir_info.py +44 -0
  678. tooluniverse/tools/get_pandas_info.py +49 -0
  679. tooluniverse/tools/get_patsy_info.py +44 -0
  680. tooluniverse/tools/get_pdbfixer_info.py +46 -0
  681. tooluniverse/tools/get_phenotype_by_HPO_ID.py +46 -0
  682. tooluniverse/tools/get_pillow_info.py +44 -0
  683. tooluniverse/tools/get_plantcv_info.py +46 -0
  684. tooluniverse/tools/get_plip_info.py +46 -0
  685. tooluniverse/tools/get_plotly_info.py +44 -0
  686. tooluniverse/tools/get_poliastro_info.py +46 -0
  687. tooluniverse/tools/get_polymer_entity_annotations.py +49 -0
  688. tooluniverse/tools/get_polymer_entity_count_by_pdb_id.py +46 -0
  689. tooluniverse/tools/get_polymer_entity_ids_by_pdb_id.py +46 -0
  690. tooluniverse/tools/get_polymer_entity_type_by_entity_id.py +49 -0
  691. tooluniverse/tools/get_polymer_molecular_weight_by_entity_id.py +49 -0
  692. tooluniverse/tools/get_poretools_info.py +44 -0
  693. tooluniverse/tools/get_prody_info.py +46 -0
  694. tooluniverse/tools/get_protein_classification_by_pdb_id.py +49 -0
  695. tooluniverse/tools/get_protein_metadata_by_pdb_id.py +46 -0
  696. tooluniverse/tools/get_pubchempy_info.py +44 -0
  697. tooluniverse/tools/get_pybedtools_info.py +49 -0
  698. tooluniverse/tools/get_pybigwig_info.py +46 -0
  699. tooluniverse/tools/get_pydeseq2_info.py +46 -0
  700. tooluniverse/tools/get_pyensembl_info.py +44 -0
  701. tooluniverse/tools/get_pyephem_info.py +44 -0
  702. tooluniverse/tools/get_pyfaidx_info.py +49 -0
  703. tooluniverse/tools/get_pyfasta_info.py +44 -0
  704. tooluniverse/tools/get_pykalman_info.py +46 -0
  705. tooluniverse/tools/get_pyliftover_info.py +49 -0
  706. tooluniverse/tools/get_pymassspec_info.py +46 -0
  707. tooluniverse/tools/get_pymed_info.py +46 -0
  708. tooluniverse/tools/get_pymzml_info.py +46 -0
  709. tooluniverse/tools/get_pypdf2_info.py +46 -0
  710. tooluniverse/tools/get_pyranges_info.py +49 -0
  711. tooluniverse/tools/get_pyrosetta_info.py +44 -0
  712. tooluniverse/tools/get_pysam_info.py +46 -0
  713. tooluniverse/tools/get_pyscenic_info.py +46 -0
  714. tooluniverse/tools/get_pyscf_info.py +46 -0
  715. tooluniverse/tools/get_pyscreener_info.py +46 -0
  716. tooluniverse/tools/get_pytdc_info.py +46 -0
  717. tooluniverse/tools/get_python_libsbml_info.py +46 -0
  718. tooluniverse/tools/get_pytorch_info.py +49 -0
  719. tooluniverse/tools/get_pyvcf_info.py +44 -0
  720. tooluniverse/tools/get_pyvis_info.py +44 -0
  721. tooluniverse/tools/get_qutip_info.py +44 -0
  722. tooluniverse/tools/get_rasterio_info.py +44 -0
  723. tooluniverse/tools/get_rdkit_info.py +46 -0
  724. tooluniverse/tools/get_refinement_resolution_by_pdb_id.py +49 -0
  725. tooluniverse/tools/get_release_deposit_dates_by_pdb_id.py +49 -0
  726. tooluniverse/tools/get_reportlab_info.py +49 -0
  727. tooluniverse/tools/get_requests_info.py +49 -0
  728. tooluniverse/tools/get_ruptures_info.py +46 -0
  729. tooluniverse/tools/get_scanorama_info.py +44 -0
  730. tooluniverse/tools/get_scanpy_info.py +49 -0
  731. tooluniverse/tools/get_schnetpack_info.py +49 -0
  732. tooluniverse/tools/get_scholarly_info.py +46 -0
  733. tooluniverse/tools/get_scikit_bio_info.py +49 -0
  734. tooluniverse/tools/get_scikit_image_info.py +46 -0
  735. tooluniverse/tools/get_scikit_learn_info.py +49 -0
  736. tooluniverse/tools/get_scipy_info.py +46 -0
  737. tooluniverse/tools/get_scrublet_info.py +49 -0
  738. tooluniverse/tools/get_scvelo_info.py +49 -0
  739. tooluniverse/tools/get_scvi_tools_info.py +44 -0
  740. tooluniverse/tools/get_seaborn_info.py +49 -0
  741. tooluniverse/tools/get_sequence_by_pdb_id.py +46 -0
  742. tooluniverse/tools/get_sequence_lengths_by_pdb_id.py +46 -0
  743. tooluniverse/tools/get_sequence_positional_features_by_instance_id.py +49 -0
  744. tooluniverse/tools/get_skopt_info.py +44 -0
  745. tooluniverse/tools/get_souporcell_info.py +46 -0
  746. tooluniverse/tools/get_source_organism_by_pdb_id.py +46 -0
  747. tooluniverse/tools/get_space_group_by_pdb_id.py +46 -0
  748. tooluniverse/tools/get_statsmodels_info.py +49 -0
  749. tooluniverse/tools/get_structure_determination_software_by_pdb_id.py +49 -0
  750. tooluniverse/tools/get_structure_title_by_pdb_id.py +46 -0
  751. tooluniverse/tools/get_structure_validation_metrics_by_pdb_id.py +49 -0
  752. tooluniverse/tools/get_sunpy_info.py +44 -0
  753. tooluniverse/tools/get_sympy_info.py +46 -0
  754. tooluniverse/tools/get_target_cofactor_info.py +46 -0
  755. tooluniverse/tools/get_taxonomy_by_pdb_id.py +46 -0
  756. tooluniverse/tools/get_tiledb_info.py +46 -0
  757. tooluniverse/tools/get_tiledbsoma_info.py +46 -0
  758. tooluniverse/tools/get_torch_geometric_info.py +49 -0
  759. tooluniverse/tools/get_tqdm_info.py +46 -0
  760. tooluniverse/tools/get_trackpy_info.py +46 -0
  761. tooluniverse/tools/get_tskit_info.py +46 -0
  762. tooluniverse/tools/get_umap_learn_info.py +49 -0
  763. tooluniverse/tools/get_uniprot_accession_by_entity_id.py +49 -0
  764. tooluniverse/tools/get_velocyto_info.py +44 -0
  765. tooluniverse/tools/get_viennarna_info.py +49 -0
  766. tooluniverse/tools/get_webpage_text_from_url.py +52 -0
  767. tooluniverse/tools/get_webpage_title.py +49 -0
  768. tooluniverse/tools/get_xarray_info.py +44 -0
  769. tooluniverse/tools/get_xesmf_info.py +44 -0
  770. tooluniverse/tools/get_xgboost_info.py +44 -0
  771. tooluniverse/tools/get_zarr_info.py +44 -0
  772. tooluniverse/tools/gnomAD_query_variant.py +52 -0
  773. tooluniverse/tools/gwas_get_association_by_id.py +49 -0
  774. tooluniverse/tools/gwas_get_associations_for_snp.py +67 -0
  775. tooluniverse/tools/gwas_get_associations_for_study.py +55 -0
  776. tooluniverse/tools/gwas_get_associations_for_trait.py +55 -0
  777. tooluniverse/tools/gwas_get_snp_by_id.py +46 -0
  778. tooluniverse/tools/gwas_get_snps_for_gene.py +55 -0
  779. tooluniverse/tools/gwas_get_studies_for_trait.py +75 -0
  780. tooluniverse/tools/gwas_get_study_by_id.py +46 -0
  781. tooluniverse/tools/gwas_get_variants_for_trait.py +55 -0
  782. tooluniverse/tools/gwas_search_associations.py +75 -0
  783. tooluniverse/tools/gwas_search_snps.py +63 -0
  784. tooluniverse/tools/gwas_search_studies.py +75 -0
  785. tooluniverse/tools/humanbase_ppi_analysis.py +67 -0
  786. tooluniverse/tools/mesh_get_subjects_by_pharmacological_action.py +63 -0
  787. tooluniverse/tools/mesh_get_subjects_by_subject_id.py +63 -0
  788. tooluniverse/tools/mesh_get_subjects_by_subject_name.py +63 -0
  789. tooluniverse/tools/mesh_get_subjects_by_subject_scope_or_definition.py +63 -0
  790. tooluniverse/tools/odphp_itemlist.py +49 -0
  791. tooluniverse/tools/odphp_myhealthfinder.py +67 -0
  792. tooluniverse/tools/odphp_outlink_fetch.py +59 -0
  793. tooluniverse/tools/odphp_topicsearch.py +67 -0
  794. tooluniverse/tools/openalex_literature_search.py +67 -0
  795. tooluniverse/tools/reactome_disease_target_score.py +52 -0
  796. tooluniverse/tools/search_clinical_trials.py +67 -0
  797. tooluniverse/tools/visualize_molecule_2d.py +83 -0
  798. tooluniverse/tools/visualize_molecule_3d.py +91 -0
  799. tooluniverse/tools/visualize_protein_structure_3d.py +79 -0
  800. tooluniverse/ucsc_tool.py +60 -0
  801. tooluniverse/unified_guideline_tools.py +2328 -0
  802. tooluniverse/unpaywall_tool.py +0 -1
  803. tooluniverse/utils.py +122 -6
  804. tooluniverse/visualization_tool.py +897 -0
  805. tooluniverse/wikidata_sparql_tool.py +1 -2
  806. tooluniverse/zenodo_tool.py +3 -4
  807. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/METADATA +19 -4
  808. tooluniverse-1.0.8.dist-info/RECORD +891 -0
  809. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/entry_points.txt +3 -0
  810. tooluniverse/test/list_azure_openai_models.py +0 -210
  811. tooluniverse/test/mcp_server_test.py +0 -0
  812. tooluniverse/test/test_admetai_tool.py +0 -370
  813. tooluniverse/test/test_agentic_tool.py +0 -129
  814. tooluniverse/test/test_agentic_tool_azure_models.py +0 -91
  815. tooluniverse/test/test_alphafold_tool.py +0 -108
  816. tooluniverse/test/test_api_key_validation_min.py +0 -64
  817. tooluniverse/test/test_chem_tool.py +0 -37
  818. tooluniverse/test/test_claude_sdk.py +0 -93
  819. tooluniverse/test/test_compose_lieraturereview.py +0 -63
  820. tooluniverse/test/test_compose_tool.py +0 -448
  821. tooluniverse/test/test_dailymed.py +0 -69
  822. tooluniverse/test/test_dataset_tool.py +0 -200
  823. tooluniverse/test/test_disease_target_score.py +0 -56
  824. tooluniverse/test/test_drugbank_filter_examples.py +0 -179
  825. tooluniverse/test/test_efo.py +0 -31
  826. tooluniverse/test/test_enrichr_tool.py +0 -21
  827. tooluniverse/test/test_europe_pmc_tool.py +0 -20
  828. tooluniverse/test/test_fda_adv.py +0 -95
  829. tooluniverse/test/test_fda_drug_labeling.py +0 -91
  830. tooluniverse/test/test_gene_ontology_tools.py +0 -66
  831. tooluniverse/test/test_global_fallback.py +0 -288
  832. tooluniverse/test/test_gwas_tool.py +0 -139
  833. tooluniverse/test/test_hooks_direct.py +0 -219
  834. tooluniverse/test/test_hpa.py +0 -625
  835. tooluniverse/test/test_humanbase_tool.py +0 -20
  836. tooluniverse/test/test_idmap_tools.py +0 -61
  837. tooluniverse/test/test_list_built_in_tools.py +0 -33
  838. tooluniverse/test/test_mcp_server.py +0 -211
  839. tooluniverse/test/test_mcp_tool.py +0 -247
  840. tooluniverse/test/test_medlineplus.py +0 -220
  841. tooluniverse/test/test_odphp_tool.py +0 -166
  842. tooluniverse/test/test_openalex_tool.py +0 -32
  843. tooluniverse/test/test_openrouter_client.py +0 -288
  844. tooluniverse/test/test_opentargets.py +0 -28
  845. tooluniverse/test/test_pubchem_tool.py +0 -116
  846. tooluniverse/test/test_pubtator_tool.py +0 -37
  847. tooluniverse/test/test_rcsb_pdb_tool.py +0 -86
  848. tooluniverse/test/test_reactome.py +0 -54
  849. tooluniverse/test/test_semantic_scholar_tool.py +0 -24
  850. tooluniverse/test/test_software_tools.py +0 -147
  851. tooluniverse/test/test_stdio_hooks.py +0 -285
  852. tooluniverse/test/test_tool_description_optimizer.py +0 -49
  853. tooluniverse/test/test_tool_finder.py +0 -26
  854. tooluniverse/test/test_tool_finder_llm.py +0 -252
  855. tooluniverse/test/test_tools_find.py +0 -195
  856. tooluniverse/test/test_uniprot_tools.py +0 -74
  857. tooluniverse/test/test_uspto_tool.py +0 -72
  858. tooluniverse/test/test_xml_tool.py +0 -113
  859. tooluniverse-1.0.6.dist-info/RECORD +0 -230
  860. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/WHEEL +0 -0
  861. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/licenses/LICENSE +0 -0
  862. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/top_level.txt +0 -0
@@ -0,0 +1,67 @@
1
+ """
2
+ ToolDescriptionOptimizer
3
+
4
+ Optimizes a tool's description and parameter descriptions by generating test cases, executing the...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolDescriptionOptimizer(
12
+ tool_config: dict[str, Any],
13
+ save_to_file: bool,
14
+ output_file: str,
15
+ max_iterations: int,
16
+ satisfaction_threshold: float,
17
+ *,
18
+ stream_callback: Optional[Callable[[str], None]] = None,
19
+ use_cache: bool = False,
20
+ validate: bool = True,
21
+ ) -> Any:
22
+ """
23
+ Optimizes a tool's description and parameter descriptions by generating test cases, executing the...
24
+
25
+ Parameters
26
+ ----------
27
+ tool_config : dict[str, Any]
28
+ The full configuration of the tool to optimize.
29
+ save_to_file : bool
30
+ If true, save the optimized description to a file (do not overwrite the origi...
31
+ output_file : str
32
+ Optional file path to save the optimized description. If not provided, use '<...
33
+ max_iterations : int
34
+ Maximum number of optimization rounds to perform.
35
+ satisfaction_threshold : float
36
+ Quality score threshold (1-10) to consider optimization satisfactory.
37
+ stream_callback : Callable, optional
38
+ Callback for streaming output
39
+ use_cache : bool, default False
40
+ Enable caching
41
+ validate : bool, default True
42
+ Validate parameters
43
+
44
+ Returns
45
+ -------
46
+ Any
47
+ """
48
+ # Handle mutable defaults to avoid B006 linting error
49
+
50
+ return get_shared_client().run_one_function(
51
+ {
52
+ "name": "ToolDescriptionOptimizer",
53
+ "arguments": {
54
+ "tool_config": tool_config,
55
+ "save_to_file": save_to_file,
56
+ "output_file": output_file,
57
+ "max_iterations": max_iterations,
58
+ "satisfaction_threshold": satisfaction_threshold,
59
+ },
60
+ },
61
+ stream_callback=stream_callback,
62
+ use_cache=use_cache,
63
+ validate=validate,
64
+ )
65
+
66
+
67
+ __all__ = ["ToolDescriptionOptimizer"]
@@ -0,0 +1,63 @@
1
+ """
2
+ ToolDiscover
3
+
4
+ Generates new ToolUniverse-compliant tools based on short descriptions through an intelligent dis...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolDiscover(
12
+ tool_description: str,
13
+ max_iterations: int,
14
+ save_to_file: bool,
15
+ output_file: str,
16
+ *,
17
+ stream_callback: Optional[Callable[[str], None]] = None,
18
+ use_cache: bool = False,
19
+ validate: bool = True,
20
+ ) -> Any:
21
+ """
22
+ Generates new ToolUniverse-compliant tools based on short descriptions through an intelligent dis...
23
+
24
+ Parameters
25
+ ----------
26
+ tool_description : str
27
+ Short description of the desired tool functionality and purpose. Tool Discove...
28
+ max_iterations : int
29
+ Maximum number of refinement iterations to perform.
30
+ save_to_file : bool
31
+ Whether to save the generated tool configuration and report to a file.
32
+ output_file : str
33
+ Optional file path to save the generated tool. If not provided, uses auto-gen...
34
+ stream_callback : Callable, optional
35
+ Callback for streaming output
36
+ use_cache : bool, default False
37
+ Enable caching
38
+ validate : bool, default True
39
+ Validate parameters
40
+
41
+ Returns
42
+ -------
43
+ Any
44
+ """
45
+ # Handle mutable defaults to avoid B006 linting error
46
+
47
+ return get_shared_client().run_one_function(
48
+ {
49
+ "name": "ToolDiscover",
50
+ "arguments": {
51
+ "tool_description": tool_description,
52
+ "max_iterations": max_iterations,
53
+ "save_to_file": save_to_file,
54
+ "output_file": output_file,
55
+ },
56
+ },
57
+ stream_callback=stream_callback,
58
+ use_cache=use_cache,
59
+ validate=validate,
60
+ )
61
+
62
+
63
+ __all__ = ["ToolDiscover"]
@@ -0,0 +1,71 @@
1
+ """
2
+ ToolGraphComposer
3
+
4
+ Builds a comprehensive graph of tool compatibility relationships in ToolUniverse. Analyzes all av...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolGraphComposer(
12
+ output_path: str,
13
+ analysis_depth: str,
14
+ min_compatibility_score: int,
15
+ exclude_categories: list[Any],
16
+ max_tools_per_category: int,
17
+ force_rebuild: bool,
18
+ *,
19
+ stream_callback: Optional[Callable[[str], None]] = None,
20
+ use_cache: bool = False,
21
+ validate: bool = True,
22
+ ) -> Any:
23
+ """
24
+ Builds a comprehensive graph of tool compatibility relationships in ToolUniverse. Analyzes all av...
25
+
26
+ Parameters
27
+ ----------
28
+ output_path : str
29
+ Path to save the generated graph files (JSON and pickle formats)
30
+ analysis_depth : str
31
+ Level of compatibility analysis to perform
32
+ min_compatibility_score : int
33
+ Minimum compatibility score to create an edge in the graph
34
+ exclude_categories : list[Any]
35
+ Tool categories to exclude from analysis (e.g., ['tool_finder', 'special_tool...
36
+ max_tools_per_category : int
37
+ Maximum number of tools to analyze per category (for performance)
38
+ force_rebuild : bool
39
+ Whether to force rebuild even if cached graph exists
40
+ stream_callback : Callable, optional
41
+ Callback for streaming output
42
+ use_cache : bool, default False
43
+ Enable caching
44
+ validate : bool, default True
45
+ Validate parameters
46
+
47
+ Returns
48
+ -------
49
+ Any
50
+ """
51
+ # Handle mutable defaults to avoid B006 linting error
52
+
53
+ return get_shared_client().run_one_function(
54
+ {
55
+ "name": "ToolGraphComposer",
56
+ "arguments": {
57
+ "output_path": output_path,
58
+ "analysis_depth": analysis_depth,
59
+ "min_compatibility_score": min_compatibility_score,
60
+ "exclude_categories": exclude_categories,
61
+ "max_tools_per_category": max_tools_per_category,
62
+ "force_rebuild": force_rebuild,
63
+ },
64
+ },
65
+ stream_callback=stream_callback,
66
+ use_cache=use_cache,
67
+ validate=validate,
68
+ )
69
+
70
+
71
+ __all__ = ["ToolGraphComposer"]
@@ -0,0 +1,63 @@
1
+ """
2
+ ToolGraphGenerationPipeline
3
+
4
+ Generates a directed tool relationship graph among provided tool configs using ToolRelationshipDe...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolGraphGenerationPipeline(
12
+ tool_configs: list[Any],
13
+ max_tools: int,
14
+ output_path: str,
15
+ save_intermediate_every: int,
16
+ *,
17
+ stream_callback: Optional[Callable[[str], None]] = None,
18
+ use_cache: bool = False,
19
+ validate: bool = True,
20
+ ) -> Any:
21
+ """
22
+ Generates a directed tool relationship graph among provided tool configs using ToolRelationshipDe...
23
+
24
+ Parameters
25
+ ----------
26
+ tool_configs : list[Any]
27
+ List of tool configuration objects
28
+ max_tools : int
29
+ Optional max number of tools to process (debug)
30
+ output_path : str
31
+ Path for output graph JSON
32
+ save_intermediate_every : int
33
+ Checkpoint every N processed pairs
34
+ stream_callback : Callable, optional
35
+ Callback for streaming output
36
+ use_cache : bool, default False
37
+ Enable caching
38
+ validate : bool, default True
39
+ Validate parameters
40
+
41
+ Returns
42
+ -------
43
+ Any
44
+ """
45
+ # Handle mutable defaults to avoid B006 linting error
46
+
47
+ return get_shared_client().run_one_function(
48
+ {
49
+ "name": "ToolGraphGenerationPipeline",
50
+ "arguments": {
51
+ "tool_configs": tool_configs,
52
+ "max_tools": max_tools,
53
+ "output_path": output_path,
54
+ "save_intermediate_every": save_intermediate_every,
55
+ },
56
+ },
57
+ stream_callback=stream_callback,
58
+ use_cache=use_cache,
59
+ validate=validate,
60
+ )
61
+
62
+
63
+ __all__ = ["ToolGraphGenerationPipeline"]
@@ -0,0 +1,67 @@
1
+ """
2
+ ToolImplementationGenerator
3
+
4
+ Generates domain-specific, functional code implementations based on tool descriptions and require...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolImplementationGenerator(
12
+ tool_description: str,
13
+ tool_parameters: str,
14
+ domain: Optional[str] = "general",
15
+ complexity_level: Optional[str] = "intermediate",
16
+ performance_requirements: Optional[str] = None,
17
+ *,
18
+ stream_callback: Optional[Callable[[str], None]] = None,
19
+ use_cache: bool = False,
20
+ validate: bool = True,
21
+ ) -> Any:
22
+ """
23
+ Generates domain-specific, functional code implementations based on tool descriptions and require...
24
+
25
+ Parameters
26
+ ----------
27
+ tool_description : str
28
+ Detailed description of what the tool should accomplish
29
+ tool_parameters : str
30
+ JSON string of parameter schema for the tool
31
+ domain : str
32
+ Domain area for specialized implementation
33
+ complexity_level : str
34
+ Desired complexity level of implementation
35
+ performance_requirements : str
36
+ Performance requirements or constraints
37
+ stream_callback : Callable, optional
38
+ Callback for streaming output
39
+ use_cache : bool, default False
40
+ Enable caching
41
+ validate : bool, default True
42
+ Validate parameters
43
+
44
+ Returns
45
+ -------
46
+ Any
47
+ """
48
+ # Handle mutable defaults to avoid B006 linting error
49
+
50
+ return get_shared_client().run_one_function(
51
+ {
52
+ "name": "ToolImplementationGenerator",
53
+ "arguments": {
54
+ "tool_description": tool_description,
55
+ "tool_parameters": tool_parameters,
56
+ "domain": domain,
57
+ "complexity_level": complexity_level,
58
+ "performance_requirements": performance_requirements,
59
+ },
60
+ },
61
+ stream_callback=stream_callback,
62
+ use_cache=use_cache,
63
+ validate=validate,
64
+ )
65
+
66
+
67
+ __all__ = ["ToolImplementationGenerator"]
@@ -0,0 +1,63 @@
1
+ """
2
+ ToolMetadataGenerationPipeline
3
+
4
+ Generates standardized metadata for a batch of ToolUniverse tool configurations by calling ToolMe...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolMetadataGenerationPipeline(
12
+ tool_configs: list[Any],
13
+ tool_type_mappings: dict[str, Any],
14
+ add_existing_tooluniverse_labels: bool,
15
+ max_new_tooluniverse_labels: int,
16
+ *,
17
+ stream_callback: Optional[Callable[[str], None]] = None,
18
+ use_cache: bool = False,
19
+ validate: bool = True,
20
+ ) -> Any:
21
+ """
22
+ Generates standardized metadata for a batch of ToolUniverse tool configurations by calling ToolMe...
23
+
24
+ Parameters
25
+ ----------
26
+ tool_configs : list[Any]
27
+ List of raw tool configuration JSON objects to extract and standardize metada...
28
+ tool_type_mappings : dict[str, Any]
29
+ Mapping of simplified toolType (keys) to lists of tool 'type' values belongin...
30
+ add_existing_tooluniverse_labels : bool
31
+ Whether to include labels from existing ToolUniverse tools when labeling the ...
32
+ max_new_tooluniverse_labels : int
33
+ The maximum number of new ToolUniverse labels to use in the metadata configs ...
34
+ stream_callback : Callable, optional
35
+ Callback for streaming output
36
+ use_cache : bool, default False
37
+ Enable caching
38
+ validate : bool, default True
39
+ Validate parameters
40
+
41
+ Returns
42
+ -------
43
+ Any
44
+ """
45
+ # Handle mutable defaults to avoid B006 linting error
46
+
47
+ return get_shared_client().run_one_function(
48
+ {
49
+ "name": "ToolMetadataGenerationPipeline",
50
+ "arguments": {
51
+ "tool_configs": tool_configs,
52
+ "tool_type_mappings": tool_type_mappings,
53
+ "add_existing_tooluniverse_labels": add_existing_tooluniverse_labels,
54
+ "max_new_tooluniverse_labels": max_new_tooluniverse_labels,
55
+ },
56
+ },
57
+ stream_callback=stream_callback,
58
+ use_cache=use_cache,
59
+ validate=validate,
60
+ )
61
+
62
+
63
+ __all__ = ["ToolMetadataGenerationPipeline"]
@@ -0,0 +1,55 @@
1
+ """
2
+ ToolMetadataGenerator
3
+
4
+ Generates a JSON structure with the metadata of a tool in ToolUniverse, given the JSON configurat...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolMetadataGenerator(
12
+ tool_config: str,
13
+ tool_type_mappings: Optional[dict[str, Any]] = None,
14
+ *,
15
+ stream_callback: Optional[Callable[[str], None]] = None,
16
+ use_cache: bool = False,
17
+ validate: bool = True,
18
+ ) -> Any:
19
+ """
20
+ Generates a JSON structure with the metadata of a tool in ToolUniverse, given the JSON configurat...
21
+
22
+ Parameters
23
+ ----------
24
+ tool_config : str
25
+ JSON string of the tool configuration to extract metadata from
26
+ tool_type_mappings : dict[str, Any]
27
+ A mapping from a simplified toolType to a list of tool_config.type that fall ...
28
+ stream_callback : Callable, optional
29
+ Callback for streaming output
30
+ use_cache : bool, default False
31
+ Enable caching
32
+ validate : bool, default True
33
+ Validate parameters
34
+
35
+ Returns
36
+ -------
37
+ Any
38
+ """
39
+ # Handle mutable defaults to avoid B006 linting error
40
+
41
+ return get_shared_client().run_one_function(
42
+ {
43
+ "name": "ToolMetadataGenerator",
44
+ "arguments": {
45
+ "tool_config": tool_config,
46
+ "tool_type_mappings": tool_type_mappings,
47
+ },
48
+ },
49
+ stream_callback=stream_callback,
50
+ use_cache=use_cache,
51
+ validate=validate,
52
+ )
53
+
54
+
55
+ __all__ = ["ToolMetadataGenerator"]
@@ -0,0 +1,52 @@
1
+ """
2
+ ToolMetadataStandardizer
3
+
4
+ Standardizes and groups semantically equivalent metadata strings (e.g., sources, tags) into canon...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolMetadataStandardizer(
12
+ metadata_list: list[Any],
13
+ limit: Optional[int] = None,
14
+ *,
15
+ stream_callback: Optional[Callable[[str], None]] = None,
16
+ use_cache: bool = False,
17
+ validate: bool = True,
18
+ ) -> Any:
19
+ """
20
+ Standardizes and groups semantically equivalent metadata strings (e.g., sources, tags) into canon...
21
+
22
+ Parameters
23
+ ----------
24
+ metadata_list : list[Any]
25
+ List of raw metadata strings (e.g., sources, tags) to standardize and group.
26
+ limit : int
27
+ If provided, the maximum number of canonical strings to return. The LLM will ...
28
+ stream_callback : Callable, optional
29
+ Callback for streaming output
30
+ use_cache : bool, default False
31
+ Enable caching
32
+ validate : bool, default True
33
+ Validate parameters
34
+
35
+ Returns
36
+ -------
37
+ Any
38
+ """
39
+ # Handle mutable defaults to avoid B006 linting error
40
+
41
+ return get_shared_client().run_one_function(
42
+ {
43
+ "name": "ToolMetadataStandardizer",
44
+ "arguments": {"metadata_list": metadata_list, "limit": limit},
45
+ },
46
+ stream_callback=stream_callback,
47
+ use_cache=use_cache,
48
+ validate=validate,
49
+ )
50
+
51
+
52
+ __all__ = ["ToolMetadataStandardizer"]
@@ -0,0 +1,59 @@
1
+ """
2
+ ToolOptimizer
3
+
4
+ Optimizes tool configurations based on quality feedback. Improves tool specifications and impleme...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolOptimizer(
12
+ tool_config: str,
13
+ quality_feedback: str,
14
+ optimization_target: str,
15
+ *,
16
+ stream_callback: Optional[Callable[[str], None]] = None,
17
+ use_cache: bool = False,
18
+ validate: bool = True,
19
+ ) -> Any:
20
+ """
21
+ Optimizes tool configurations based on quality feedback. Improves tool specifications and impleme...
22
+
23
+ Parameters
24
+ ----------
25
+ tool_config : str
26
+ JSON string of the original tool configuration
27
+ quality_feedback : str
28
+ JSON string of quality evaluation feedback
29
+ optimization_target : str
30
+ What to optimize for (improve_quality, enhance_performance, etc.)
31
+ stream_callback : Callable, optional
32
+ Callback for streaming output
33
+ use_cache : bool, default False
34
+ Enable caching
35
+ validate : bool, default True
36
+ Validate parameters
37
+
38
+ Returns
39
+ -------
40
+ Any
41
+ """
42
+ # Handle mutable defaults to avoid B006 linting error
43
+
44
+ return get_shared_client().run_one_function(
45
+ {
46
+ "name": "ToolOptimizer",
47
+ "arguments": {
48
+ "tool_config": tool_config,
49
+ "quality_feedback": quality_feedback,
50
+ "optimization_target": optimization_target,
51
+ },
52
+ },
53
+ stream_callback=stream_callback,
54
+ use_cache=use_cache,
55
+ validate=validate,
56
+ )
57
+
58
+
59
+ __all__ = ["ToolOptimizer"]
@@ -0,0 +1,67 @@
1
+ """
2
+ ToolOutputSummarizer
3
+
4
+ AI-powered tool for summarizing long tool outputs, focusing on key information relevant to the or...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolOutputSummarizer(
12
+ tool_output: str,
13
+ query_context: str,
14
+ tool_name: str,
15
+ focus_areas: Optional[str] = "key_findings_and_results",
16
+ max_length: Optional[int] = 32000,
17
+ *,
18
+ stream_callback: Optional[Callable[[str], None]] = None,
19
+ use_cache: bool = False,
20
+ validate: bool = True,
21
+ ) -> Any:
22
+ """
23
+ AI-powered tool for summarizing long tool outputs, focusing on key information relevant to the or...
24
+
25
+ Parameters
26
+ ----------
27
+ tool_output : str
28
+ The original tool output to be summarized
29
+ query_context : str
30
+ Context about the original query that triggered the tool
31
+ tool_name : str
32
+ Name of the tool that generated the output
33
+ focus_areas : str
34
+ Specific areas to focus on in the summary
35
+ max_length : int
36
+ Maximum length of the summary in characters
37
+ stream_callback : Callable, optional
38
+ Callback for streaming output
39
+ use_cache : bool, default False
40
+ Enable caching
41
+ validate : bool, default True
42
+ Validate parameters
43
+
44
+ Returns
45
+ -------
46
+ Any
47
+ """
48
+ # Handle mutable defaults to avoid B006 linting error
49
+
50
+ return get_shared_client().run_one_function(
51
+ {
52
+ "name": "ToolOutputSummarizer",
53
+ "arguments": {
54
+ "tool_output": tool_output,
55
+ "query_context": query_context,
56
+ "tool_name": tool_name,
57
+ "focus_areas": focus_areas,
58
+ "max_length": max_length,
59
+ },
60
+ },
61
+ stream_callback=stream_callback,
62
+ use_cache=use_cache,
63
+ validate=validate,
64
+ )
65
+
66
+
67
+ __all__ = ["ToolOutputSummarizer"]
@@ -0,0 +1,59 @@
1
+ """
2
+ ToolQualityEvaluator
3
+
4
+ Evaluates the quality of tool configurations and implementations. Provides detailed scoring and f...
5
+ """
6
+
7
+ from typing import Any, Optional, Callable
8
+ from ._shared_client import get_shared_client
9
+
10
+
11
+ def ToolQualityEvaluator(
12
+ tool_config: str,
13
+ test_cases: str,
14
+ evaluation_aspects: list[Any],
15
+ *,
16
+ stream_callback: Optional[Callable[[str], None]] = None,
17
+ use_cache: bool = False,
18
+ validate: bool = True,
19
+ ) -> Any:
20
+ """
21
+ Evaluates the quality of tool configurations and implementations. Provides detailed scoring and f...
22
+
23
+ Parameters
24
+ ----------
25
+ tool_config : str
26
+ JSON string of the tool configuration
27
+ test_cases : str
28
+ JSON string of test cases
29
+ evaluation_aspects : list[Any]
30
+ Aspects to evaluate (functionality, usability, completeness, best_practices)
31
+ stream_callback : Callable, optional
32
+ Callback for streaming output
33
+ use_cache : bool, default False
34
+ Enable caching
35
+ validate : bool, default True
36
+ Validate parameters
37
+
38
+ Returns
39
+ -------
40
+ Any
41
+ """
42
+ # Handle mutable defaults to avoid B006 linting error
43
+
44
+ return get_shared_client().run_one_function(
45
+ {
46
+ "name": "ToolQualityEvaluator",
47
+ "arguments": {
48
+ "tool_config": tool_config,
49
+ "test_cases": test_cases,
50
+ "evaluation_aspects": evaluation_aspects,
51
+ },
52
+ },
53
+ stream_callback=stream_callback,
54
+ use_cache=use_cache,
55
+ validate=validate,
56
+ )
57
+
58
+
59
+ __all__ = ["ToolQualityEvaluator"]