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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  589. tooluniverse/tools/get_clinical_trial_outcome_measures.py +52 -0
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  624. tooluniverse/tools/get_flowutils_info.py +46 -0
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  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
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  639. tooluniverse/tools/get_igraph_info.py +49 -0
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  641. tooluniverse/tools/get_imbalanced_learn_info.py +44 -0
  642. tooluniverse/tools/get_jcvi_info.py +46 -0
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  644. tooluniverse/tools/get_joint_associated_diseases_by_HPO_ID_list.py +55 -0
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  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
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  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
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  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
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  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
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  720. tooluniverse/tools/get_pyvis_info.py +44 -0
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  727. tooluniverse/tools/get_requests_info.py +49 -0
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  738. tooluniverse/tools/get_scvelo_info.py +49 -0
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  751. tooluniverse/tools/get_structure_validation_metrics_by_pdb_id.py +49 -0
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  756. tooluniverse/tools/get_tiledb_info.py +46 -0
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  772. tooluniverse/tools/gnomAD_query_variant.py +52 -0
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  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 +1,306 @@
1
+ [
2
+ {
3
+ "type": "AgenticTool",
4
+ "name": "IntentAnalyzerAgent",
5
+ "description": "AI agent that analyzes user research intent and creates comprehensive search plans",
6
+ "prompt": "Analyze this research query and create a comprehensive search strategy:\n\nQuery: \"{user_query}\"\n\nContext: {context}\n\nPlease provide:\n1. User Intent: What is the user really looking for?\n2. Search Plans: Create 3-5 specific search plans that would comprehensively cover this topic\n\nFor each search plan, provide:\n- Title: A clear, specific title\n- Description: What this plan aims to find\n- Keywords: 3-5 specific keywords for this plan\n- Priority: 1-5 (5 being highest priority)\n\nReturn as JSON format:\n{\n \"user_intent\": \"...\",\n \"search_plans\": [\n {\n \"title\": \"...\",\n \"description\": \"...\",\n \"keywords\": [\"...\", \"...\", \"...\"],\n \"priority\": 5\n }\n ]\n}",
7
+ "input_arguments": [
8
+ "user_query",
9
+ "context"
10
+ ],
11
+ "parameter": {
12
+ "type": "object",
13
+ "properties": {
14
+ "user_query": {
15
+ "type": "string",
16
+ "description": "The research query to analyze",
17
+ "required": true
18
+ },
19
+ "context": {
20
+ "type": "string",
21
+ "description": "Context information from previous steps",
22
+ "required": false,
23
+ "default": ""
24
+ }
25
+ },
26
+ "required": [
27
+ "user_query"
28
+ ]
29
+ },
30
+ "configs": {
31
+ "api_type": "CHATGPT",
32
+ "model_id": "gpt-4.1",
33
+ "temperature": 0.7,
34
+ "max_new_tokens": 2048,
35
+ "return_json": false
36
+ }
37
+ },
38
+ {
39
+ "type": "AgenticTool",
40
+ "name": "KeywordExtractorAgent",
41
+ "description": "AI agent that extracts and refines search keywords for research plans",
42
+ "prompt": "Extract and refine search keywords for this research plan:\n\nPlan Title: {plan_title}\nPlan Description: {plan_description}\nCurrent Keywords: {current_keywords}\nContext: {context}\n\nPlease provide 5-8 specific, academic search keywords that would be most effective for finding relevant papers.\nConsider:\n- Synonyms and related terms\n- Technical terminology\n- Academic language\n- Different aspects of the topic\n- Previous search results and insights from context\n\nReturn as JSON:\n{\n \"refined_keywords\": [\"keyword1\", \"keyword2\", \"keyword3\", \"keyword4\", \"keyword5\"]\n}",
43
+ "input_arguments": [
44
+ "plan_title",
45
+ "plan_description",
46
+ "current_keywords",
47
+ "context"
48
+ ],
49
+ "parameter": {
50
+ "type": "object",
51
+ "properties": {
52
+ "plan_title": {
53
+ "type": "string",
54
+ "description": "The title of the search plan",
55
+ "required": true
56
+ },
57
+ "plan_description": {
58
+ "type": "string",
59
+ "description": "The description of the search plan",
60
+ "required": true
61
+ },
62
+ "current_keywords": {
63
+ "type": "string",
64
+ "description": "Current keywords for the plan (comma-separated)",
65
+ "required": true
66
+ },
67
+ "context": {
68
+ "type": "string",
69
+ "description": "Context information from previous steps",
70
+ "required": false,
71
+ "default": ""
72
+ }
73
+ },
74
+ "required": [
75
+ "plan_title",
76
+ "plan_description",
77
+ "current_keywords"
78
+ ]
79
+ },
80
+ "configs": {
81
+ "api_type": "CHATGPT",
82
+ "model_id": "gpt-4.1",
83
+ "temperature": 0.5,
84
+ "max_new_tokens": 1024,
85
+ "return_json": false
86
+ }
87
+ },
88
+ {
89
+ "type": "AgenticTool",
90
+ "name": "ResultSummarizerAgent",
91
+ "description": "AI agent that summarizes search results for research plans",
92
+ "prompt": "Summarize the search results for this research plan:\n\nPlan Title: {plan_title}\nPlan Description: {plan_description}\nNumber of Papers: {paper_count}\nContext: {context}\n\nPapers:\n{papers_text}\n\nPlease provide a comprehensive summary that includes:\n1. Key findings and insights\n2. Main themes and trends\n3. Important papers and their contributions\n4. Research gaps or opportunities\n5. Overall assessment of the search results\n\nKeep the summary concise but informative (300-500 words).",
93
+ "input_arguments": [
94
+ "plan_title",
95
+ "plan_description",
96
+ "paper_count",
97
+ "papers_text",
98
+ "context"
99
+ ],
100
+ "parameter": {
101
+ "type": "object",
102
+ "properties": {
103
+ "plan_title": {
104
+ "type": "string",
105
+ "description": "The title of the search plan",
106
+ "required": true
107
+ },
108
+ "plan_description": {
109
+ "type": "string",
110
+ "description": "The description of the search plan",
111
+ "required": true
112
+ },
113
+ "paper_count": {
114
+ "type": "string",
115
+ "description": "Number of papers found",
116
+ "required": true
117
+ },
118
+ "papers_text": {
119
+ "type": "string",
120
+ "description": "Formatted text of the papers to summarize",
121
+ "required": true
122
+ },
123
+ "context": {
124
+ "type": "string",
125
+ "description": "Context information from previous steps",
126
+ "required": false,
127
+ "default": ""
128
+ }
129
+ },
130
+ "required": [
131
+ "plan_title",
132
+ "plan_description",
133
+ "paper_count",
134
+ "papers_text"
135
+ ]
136
+ },
137
+ "configs": {
138
+ "api_type": "CHATGPT",
139
+ "model_id": "gpt-4.1",
140
+ "temperature": 0.3,
141
+ "max_new_tokens": 1024,
142
+ "return_json": false
143
+ }
144
+ },
145
+ {
146
+ "type": "AgenticTool",
147
+ "name": "QualityCheckerAgent",
148
+ "description": "AI agent that checks search result quality and suggests improvements",
149
+ "prompt": "Based on the current search results quality assessment, suggest improvements for the next iteration:\n\nCurrent Plans and Quality Scores:\n{plans_analysis}\nContext: {context}\n\nPlease suggest:\n1. Which plans need improvement\n2. New search strategies or keywords\n3. Additional search plans if needed\n\nReturn as JSON:\n{\n \"improvements\": [\n {\n \"plan_id\": \"plan_1\",\n \"suggestions\": [\"suggestion1\", \"suggestion2\"]\n }\n ],\n \"new_plans\": [\n {\n \"title\": \"New Plan Title\",\n \"description\": \"Description\",\n \"keywords\": [\"keyword1\", \"keyword2\"],\n \"priority\": 3\n }\n ]\n}",
150
+ "input_arguments": [
151
+ "plans_analysis",
152
+ "context"
153
+ ],
154
+ "parameter": {
155
+ "type": "object",
156
+ "properties": {
157
+ "plans_analysis": {
158
+ "type": "string",
159
+ "description": "Analysis of current search plans and their quality scores",
160
+ "required": true
161
+ },
162
+ "context": {
163
+ "type": "string",
164
+ "description": "Context information from previous steps",
165
+ "required": false,
166
+ "default": ""
167
+ }
168
+ },
169
+ "required": [
170
+ "plans_analysis"
171
+ ]
172
+ },
173
+ "configs": {
174
+ "api_type": "CHATGPT",
175
+ "model_id": "gpt-4.1",
176
+ "temperature": 0.5,
177
+ "max_new_tokens": 1536,
178
+ "return_json": false
179
+ }
180
+ },
181
+ {
182
+ "type": "AgenticTool",
183
+ "name": "OverallSummaryAgent",
184
+ "description": "AI agent that generates comprehensive overall summary of multi-agent search results",
185
+ "prompt": "Generate a comprehensive overall summary of the multi-agent literature search results:\n\nResearch Query: {user_query}\nUser Intent: {user_intent}\nTotal Papers Found: {total_papers}\nSearch Plans Executed: {total_plans}\nIterations: {iterations}\nContext: {context}\n\nPlan Summaries:\n{plan_summaries}\n\nPlease provide a comprehensive summary that includes:\n1. Executive summary of findings\n2. Key research themes and trends\n3. Most important papers and their contributions\n4. Research gaps and opportunities\n5. Overall assessment and recommendations\n\nFormat as markdown with clear sections and bullet points.",
186
+ "input_arguments": [
187
+ "user_query",
188
+ "user_intent",
189
+ "total_papers",
190
+ "total_plans",
191
+ "iterations",
192
+ "plan_summaries",
193
+ "context"
194
+ ],
195
+ "parameter": {
196
+ "type": "object",
197
+ "properties": {
198
+ "user_query": {
199
+ "type": "string",
200
+ "description": "The original research query",
201
+ "required": true
202
+ },
203
+ "user_intent": {
204
+ "type": "string",
205
+ "description": "The analyzed user intent",
206
+ "required": true
207
+ },
208
+ "total_papers": {
209
+ "type": "string",
210
+ "description": "Total number of papers found",
211
+ "required": true
212
+ },
213
+ "total_plans": {
214
+ "type": "string",
215
+ "description": "Total number of search plans executed",
216
+ "required": true
217
+ },
218
+ "iterations": {
219
+ "type": "string",
220
+ "description": "Number of iterations performed",
221
+ "required": true
222
+ },
223
+ "plan_summaries": {
224
+ "type": "string",
225
+ "description": "Summaries of all search plans",
226
+ "required": true
227
+ },
228
+ "context": {
229
+ "type": "string",
230
+ "description": "Context information from previous steps",
231
+ "required": false,
232
+ "default": ""
233
+ }
234
+ },
235
+ "required": [
236
+ "user_query",
237
+ "user_intent",
238
+ "total_papers",
239
+ "total_plans",
240
+ "iterations",
241
+ "plan_summaries"
242
+ ]
243
+ },
244
+ "configs": {
245
+ "api_type": "CHATGPT",
246
+ "model_id": "gpt-4.1",
247
+ "temperature": 0.3,
248
+ "max_new_tokens": 2048,
249
+ "return_json": false
250
+ }
251
+ },
252
+ {
253
+ "type": "ComposeTool",
254
+ "name": "MultiAgentLiteratureSearch",
255
+ "description": "Multi-agent literature search system that uses AI agents to analyze intent, extract keywords, execute parallel searches, summarize results, and check quality iteratively",
256
+ "parameter": {
257
+ "type": "object",
258
+ "properties": {
259
+ "query": {
260
+ "type": "string",
261
+ "description": "The research query to search for"
262
+ },
263
+ "max_iterations": {
264
+ "type": "integer",
265
+ "description": "Maximum number of iterations (default: 3)",
266
+ "default": 3
267
+ },
268
+ "quality_threshold": {
269
+ "type": "number",
270
+ "description": "Quality threshold for completion (default: 0.7)",
271
+ "default": 0.7
272
+ }
273
+ },
274
+ "required": [
275
+ "query",
276
+ "max_iterations",
277
+ "quality_threshold"
278
+ ]
279
+ },
280
+ "auto_load_dependencies": true,
281
+ "fail_on_missing_tools": false,
282
+ "required_tools": [
283
+ "IntentAnalyzerAgent",
284
+ "KeywordExtractorAgent",
285
+ "ResultSummarizerAgent",
286
+ "QualityCheckerAgent",
287
+ "OverallSummaryAgent",
288
+ "ArXiv_search_papers",
289
+ "BioRxiv_search_preprints",
290
+ "MedRxiv_search_preprints",
291
+ "HAL_search_archive",
292
+ "Crossref_search_works",
293
+ "PubMed_search_articles",
294
+ "EuropePMC_search_articles",
295
+ "SemanticScholar_search_papers",
296
+ "openalex_literature_search",
297
+ "DBLP_search_publications",
298
+ "DOAJ_search_articles",
299
+ "CORE_search_papers",
300
+ "PMC_search_papers",
301
+ "Zenodo_search_records"
302
+ ],
303
+ "composition_file": "enhanced_multi_agent_literature_search.py",
304
+ "composition_function": "compose"
305
+ }
306
+ ]
@@ -0,0 +1,51 @@
1
+ [
2
+ {
3
+ "type": "MarkItDownTool",
4
+ "name": "convert_to_markdown",
5
+ "description": "Convert a resource described by an http:, https:, file: or data: URI to markdown.",
6
+ "parameter": {
7
+ "type": "object",
8
+ "properties": {
9
+ "uri": {
10
+ "type": "string",
11
+ "description": "URI of the resource to convert (supports http:, https:, file:, data: URIs)"
12
+ },
13
+ "output_path": {
14
+ "type": "string",
15
+ "description": "Optional output file path"
16
+ },
17
+ "enable_plugins": {
18
+ "type": "boolean",
19
+ "description": "Enable 3rd-party plugins",
20
+ "default": false
21
+ }
22
+ },
23
+ "required": ["uri"]
24
+ },
25
+ "return_schema": {
26
+ "type": "object",
27
+ "properties": {
28
+ "markdown_content": {
29
+ "type": "string",
30
+ "description": "The converted Markdown content"
31
+ },
32
+ "content": {
33
+ "type": "string",
34
+ "description": "The converted Markdown content (same as markdown_content, provided for convenience when no output_path is specified)"
35
+ },
36
+ "file_info": {
37
+ "type": "object",
38
+ "properties": {
39
+ "original_file": {"type": "string"},
40
+ "file_type": {"type": "string"},
41
+ "output_file": {"type": "string"}
42
+ }
43
+ },
44
+ "error": {
45
+ "type": "string",
46
+ "description": "Error message if conversion failed"
47
+ }
48
+ }
49
+ }
50
+ }
51
+ ]
@@ -1,113 +1,128 @@
1
1
  [
2
- {
3
- "name": "mcp_client_example",
4
- "description": "Example MCP client to connect to an existing MCP server. Supports all MCP operations including tools, resources, and prompts.",
5
- "type": "MCPClientTool",
6
- "server_url": "http://localhost:8000",
7
- "transport": "http",
8
- "parameter": {
9
- "type": "object",
10
- "properties": {
11
- "operation": {
12
- "type": "string",
13
- "enum": ["list_tools", "call_tool", "list_resources", "read_resource", "list_prompts", "get_prompt"],
14
- "description": "The MCP operation to perform"
15
- },
16
- "tool_name": {
17
- "type": "string",
18
- "description": "Name of the tool to call (required for call_tool operation)"
19
- },
20
- "tool_arguments": {
21
- "type": "object",
22
- "description": "Arguments to pass to the tool (for call_tool operation)"
23
- },
24
- "uri": {
25
- "type": "string",
26
- "description": "Resource URI (required for read_resource operation)"
27
- },
28
- "prompt_name": {
29
- "type": "string",
30
- "description": "Name of the prompt to get (required for get_prompt operation)"
31
- },
32
- "prompt_arguments": {
33
- "type": "object",
34
- "description": "Arguments to pass to the prompt (for get_prompt operation)"
35
- }
36
- },
37
- "required": ["operation"]
2
+ {
3
+ "name": "mcp_client_example",
4
+ "description": "Example MCP client to connect to an existing MCP server. Supports all MCP operations including tools, resources, and prompts.",
5
+ "type": "MCPClientTool",
6
+ "server_url": "http://localhost:8000",
7
+ "transport": "http",
8
+ "parameter": {
9
+ "type": "object",
10
+ "properties": {
11
+ "operation": {
12
+ "type": "string",
13
+ "enum": [
14
+ "list_tools",
15
+ "call_tool",
16
+ "list_resources",
17
+ "read_resource",
18
+ "list_prompts",
19
+ "get_prompt"
20
+ ],
21
+ "description": "The MCP operation to perform"
22
+ },
23
+ "tool_name": {
24
+ "type": "string",
25
+ "description": "Name of the tool to call (required for call_tool operation)"
26
+ },
27
+ "tool_arguments": {
28
+ "type": "object",
29
+ "description": "Arguments to pass to the tool (for call_tool operation)"
30
+ },
31
+ "uri": {
32
+ "type": "string",
33
+ "description": "Resource URI (required for read_resource operation)"
34
+ },
35
+ "prompt_name": {
36
+ "type": "string",
37
+ "description": "Name of the prompt to get (required for get_prompt operation)"
38
+ },
39
+ "prompt_arguments": {
40
+ "type": "object",
41
+ "description": "Arguments to pass to the prompt (for get_prompt operation)"
38
42
  }
39
- },
40
- {
41
- "name": "mcp_mock_calculator",
42
- "description": "A simple calculator tool for testing",
43
- "type": "MCPProxyTool",
44
- "server_url": "http://localhost:8000",
45
- "transport": "http",
46
- "target_tool_name": "mock_calculator",
47
- "parameter": {
48
- "type": "object",
49
- "properties": {
50
- "operation": {
51
- "type": "string",
52
- "enum": [
53
- "add",
54
- "subtract",
55
- "multiply",
56
- "divide"
57
- ],
58
- "description": "The mathematical operation to perform"
59
- },
60
- "a": {
61
- "type": "number",
62
- "description": "First number"
63
- },
64
- "b": {
65
- "type": "number",
66
- "description": "Second number"
67
- }
68
- },
69
- "required": [
70
- "operation",
71
- "a",
72
- "b"
73
- ]
43
+ },
44
+ "required": [
45
+ "operation",
46
+ "tool_name",
47
+ "tool_arguments",
48
+ "uri",
49
+ "prompt_name",
50
+ "prompt_arguments"
51
+ ]
52
+ }
53
+ },
54
+ {
55
+ "name": "mcp_mock_calculator",
56
+ "description": "A simple calculator tool for testing",
57
+ "type": "MCPProxyTool",
58
+ "server_url": "http://localhost:8000",
59
+ "transport": "http",
60
+ "target_tool_name": "mock_calculator",
61
+ "parameter": {
62
+ "type": "object",
63
+ "properties": {
64
+ "operation": {
65
+ "type": "string",
66
+ "enum": [
67
+ "add",
68
+ "subtract",
69
+ "multiply",
70
+ "divide"
71
+ ],
72
+ "description": "The mathematical operation to perform"
73
+ },
74
+ "a": {
75
+ "type": "number",
76
+ "description": "First number"
77
+ },
78
+ "b": {
79
+ "type": "number",
80
+ "description": "Second number"
74
81
  }
75
- },
76
- {
77
- "name": "mcp_mock_greeter",
78
- "description": "A simple greeting tool",
79
- "type": "MCPProxyTool",
80
- "server_url": "http://localhost:8000",
81
- "transport": "http",
82
- "target_tool_name": "mock_greeter",
83
- "parameter": {
84
- "type": "object",
85
- "properties": {
86
- "name": {
87
- "type": "string",
88
- "description": "Name to greet"
89
- },
90
- "language": {
91
- "type": "string",
92
- "enum": [
93
- "en",
94
- "es",
95
- "fr"
96
- ],
97
- "description": "Language for greeting",
98
- "default": "en"
99
- }
100
- },
101
- "required": [
102
- "name"
103
- ]
82
+ },
83
+ "required": [
84
+ "operation",
85
+ "a",
86
+ "b"
87
+ ]
88
+ }
89
+ },
90
+ {
91
+ "name": "mcp_mock_greeter",
92
+ "description": "A simple greeting tool",
93
+ "type": "MCPProxyTool",
94
+ "server_url": "http://localhost:8000",
95
+ "transport": "http",
96
+ "target_tool_name": "mock_greeter",
97
+ "parameter": {
98
+ "type": "object",
99
+ "properties": {
100
+ "name": {
101
+ "type": "string",
102
+ "description": "Name to greet"
103
+ },
104
+ "language": {
105
+ "type": "string",
106
+ "enum": [
107
+ "en",
108
+ "es",
109
+ "fr"
110
+ ],
111
+ "description": "Language for greeting",
112
+ "default": "en"
104
113
  }
105
- },
106
- {
107
- "name": "mcp_auto_loader_server1",
108
- "description": "Automatically discover and load all tools from MCP Server 1. Can register discovered tools as individual ToolUniverse tools or provide tool configurations.",
109
- "type": "MCPAutoLoaderTool",
110
- "server_url": "http://localhost:8000",
111
- "tool_prefix": "mcp_s1_"
114
+ },
115
+ "required": [
116
+ "name",
117
+ "language"
118
+ ]
112
119
  }
120
+ },
121
+ {
122
+ "name": "mcp_auto_loader_server1",
123
+ "description": "Automatically discover and load all tools from MCP Server 1. Can register discovered tools as individual ToolUniverse tools or provide tool configurations.",
124
+ "type": "MCPAutoLoaderTool",
125
+ "server_url": "http://localhost:8000",
126
+ "tool_prefix": "mcp_s1_"
127
+ }
113
128
  ]