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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  581. tooluniverse/tools/get_chem_comp_charge_and_ambiguity.py +46 -0
  582. tooluniverse/tools/get_chembl_webresource_client_info.py +44 -0
  583. tooluniverse/tools/get_citation_info_by_pdb_id.py +46 -0
  584. tooluniverse/tools/get_clair3_info.py +46 -0
  585. tooluniverse/tools/get_clinical_trial_conditions_and_interventions.py +55 -0
  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
  592. tooluniverse/tools/get_cobra_info.py +46 -0
  593. tooluniverse/tools/get_cobrapy_info.py +46 -0
  594. tooluniverse/tools/get_cooler_info.py +49 -0
  595. tooluniverse/tools/get_core_refinement_statistics.py +46 -0
  596. tooluniverse/tools/get_cryosparc_tools_info.py +46 -0
  597. tooluniverse/tools/get_crystal_growth_conditions_by_pdb_id.py +49 -0
  598. tooluniverse/tools/get_crystallization_ph_by_pdb_id.py +46 -0
  599. tooluniverse/tools/get_crystallographic_properties_by_pdb_id.py +49 -0
  600. tooluniverse/tools/get_cupy_info.py +44 -0
  601. tooluniverse/tools/get_cyvcf2_info.py +49 -0
  602. tooluniverse/tools/get_dask_info.py +44 -0
  603. tooluniverse/tools/get_datamol_info.py +44 -0
  604. tooluniverse/tools/get_datashader_info.py +44 -0
  605. tooluniverse/tools/get_deepchem_info.py +49 -0
  606. tooluniverse/tools/get_deeppurpose_info.py +46 -0
  607. tooluniverse/tools/get_deeptools_info.py +46 -0
  608. tooluniverse/tools/get_deepxde_info.py +49 -0
  609. tooluniverse/tools/get_dendropy_info.py +44 -0
  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
  617. tooluniverse/tools/get_episcanpy_info.py +44 -0
  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
@@ -1,200 +0,0 @@
1
- from tooluniverse import ToolUniverse
2
-
3
- # Step 1: Initialize tool universe
4
- tooluni = ToolUniverse()
5
- tooluni.load_tools()
6
-
7
- test_queries = [
8
- # Test 1: Search for a specific drug by name
9
- {"name": "drugbank_vocab_search", "arguments": {"query": "aspirin"}},
10
- # Test 2: Exact match search for a DrugBank ID
11
- {
12
- "name": "drugbank_vocab_search",
13
- "arguments": {
14
- "query": "DB00001",
15
- "search_fields": ["DrugBank ID"],
16
- "exact_match": True,
17
- },
18
- },
19
- # Test 3: Search in synonyms with case sensitivity
20
- {
21
- "name": "drugbank_vocab_search",
22
- "arguments": {
23
- "query": "Lepirudin",
24
- "search_fields": ["Synonyms", "Common name"],
25
- "case_sensitive": True,
26
- "limit": 10,
27
- },
28
- },
29
- # Test 4: Filter drugs that have CAS numbers
30
- {
31
- "name": "drugbank_vocab_filter",
32
- "arguments": {"field": "CAS", "condition": "not_empty", "limit": 5},
33
- },
34
- # Test 5: Filter drugs starting with "DB000"
35
- {
36
- "name": "drugbank_vocab_filter",
37
- "arguments": {
38
- "field": "DrugBank ID",
39
- "condition": "starts_with",
40
- "value": "DB000",
41
- "limit": 10,
42
- },
43
- },
44
- # Test 6: Filter drugs containing "interferon" in common name
45
- {
46
- "name": "drugbank_vocab_filter",
47
- "arguments": {
48
- "field": "Common name",
49
- "condition": "contains",
50
- "value": "interferon",
51
- "limit": 5,
52
- },
53
- },
54
- # Test 7: Complex search with multiple fields
55
- {
56
- "name": "drugbank_vocab_search",
57
- "arguments": {
58
- "query": "insulin",
59
- "search_fields": ["Common name", "Synonyms"],
60
- "case_sensitive": False,
61
- "exact_match": False,
62
- "limit": 3,
63
- },
64
- },
65
- # ---------- drugbank_full_search ----------
66
- # 1. Partial common-name query
67
- {
68
- "name": "drugbank_full_search",
69
- "arguments": {
70
- "query": "acetylsalicylic",
71
- "search_fields": ["name"],
72
- "limit": 5,
73
- },
74
- },
75
- # 2. Exact-match lookup by DrugBank ID
76
- {
77
- "name": "drugbank_full_search",
78
- "arguments": {
79
- "query": "DB00003",
80
- "search_fields": ["drugbank_id"],
81
- "exact_match": True,
82
- },
83
- },
84
- # 3. Case-sensitive synonym search
85
- {
86
- "name": "drugbank_full_search",
87
- "arguments": {
88
- "query": "Olanzapine",
89
- "search_fields": ["synonyms"],
90
- "case_sensitive": True,
91
- "limit": 3,
92
- },
93
- },
94
- # ---------- drugbank_links_search ----------
95
- # 4. Exact CAS-number lookup
96
- {
97
- "name": "drugbank_links_search",
98
- "arguments": {
99
- "query": "205923-56-4",
100
- "search_fields": ["CAS Number"],
101
- "exact_match": True,
102
- },
103
- },
104
- # 5. Search by PharmGKB identifier
105
- {
106
- "name": "drugbank_links_search",
107
- "arguments": {"query": "PA10040", "search_fields": ["PharmGKB ID"]},
108
- },
109
- # 6. Search by KEGG Drug ID
110
- {
111
- "name": "drugbank_links_search",
112
- "arguments": {"query": "D03455", "search_fields": ["KEGG Drug ID"]},
113
- },
114
- # ---------- dict_search (DICTrank) ----------
115
- # 7. Search by trade name
116
- {
117
- "name": "dict_search",
118
- "arguments": {"query": "ZYPREXA", "search_fields": ["Trade Name"], "limit": 2},
119
- },
120
- # 8. Search by active ingredient (case-insensitive)
121
- {
122
- "name": "dict_search",
123
- "arguments": {
124
- "query": "trimethobenzamide",
125
- "search_fields": ["Active Ingredient(s)"],
126
- "case_sensitive": False,
127
- },
128
- },
129
- # ---------- dili_search (DILIrank) ----------
130
- # 9. Exact compound-name search
131
- {
132
- "name": "dili_search",
133
- "arguments": {
134
- "query": "acetaminophen",
135
- "search_fields": ["Compound Name"],
136
- "exact_match": True,
137
- },
138
- },
139
- # 10. Partial compound-name query
140
- {
141
- "name": "dili_search",
142
- "arguments": {
143
- "query": "mercap",
144
- "search_fields": ["Compound Name"],
145
- "limit": 5,
146
- },
147
- },
148
- # ---------- diqt_search (DIQTA) ----------
149
- # 11. Exact DrugBank ID lookup
150
- {
151
- "name": "diqt_search",
152
- "arguments": {
153
- "query": "DB00637",
154
- "search_fields": ["DrugBank ID"],
155
- "exact_match": True,
156
- },
157
- },
158
- # 12. Generic name search (case-insensitive)
159
- {
160
- "name": "diqt_search",
161
- "arguments": {
162
- "query": "dofetilide",
163
- "search_fields": ["Generic/Proper Name(s)"],
164
- "case_sensitive": False,
165
- },
166
- },
167
- ]
168
-
169
- for idx, query in enumerate(test_queries):
170
- print(
171
- f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
172
- )
173
- try:
174
- result = tooluni.run(query)
175
- print("✅ Success. Example output snippet:")
176
-
177
- # Pretty print the result based on its structure
178
- if isinstance(result, dict):
179
- if "results" in result:
180
- print(
181
- f"Found {result.get('total_results', result.get('total_matches', 0))} results"
182
- )
183
- if result["results"]:
184
- # Show first result
185
- first_result = result["results"][0]
186
- # print(f"First result: {first_result.get('Common name', 'N/A')} (ID: {first_result.get('DrugBank ID', 'N/A')})")
187
- print(f"First result: {first_result})")
188
- if "matched_fields" in first_result:
189
- print(f"Matched fields: {first_result['matched_fields']}")
190
- elif "error" in result:
191
- print(f"Error: {result['error']}")
192
- else:
193
- print(
194
- str(result)[:200] + "..." if len(str(result)) > 200 else str(result)
195
- )
196
- else:
197
- print(str(result)[:200] + "..." if len(str(result)) > 200 else str(result))
198
-
199
- except Exception as e:
200
- print(f"❌ Error: {e}")
@@ -1,56 +0,0 @@
1
- #!/usr/bin/env python3
2
- """
3
- Simple test for disease-target score extraction tools.
4
- """
5
-
6
- import sys
7
- import os
8
-
9
- # Add the src directory to the path
10
- sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", "src"))
11
-
12
- from tooluniverse import ToolUniverse # noqa: E402
13
-
14
-
15
- def test_disease_target_score_tools():
16
- """Test the disease-target score extraction tools"""
17
- print("Testing Disease-Target Score Tools...")
18
-
19
- # Initialize ToolUniverse and load all tools
20
- engine = ToolUniverse()
21
- engine.load_tools()
22
-
23
- # Test both generic and specific tools
24
- tests = [
25
- (
26
- "generic tool",
27
- "disease_target_score",
28
- {"efoId": "EFO_0000339", "datasourceId": "impc"},
29
- ),
30
- (
31
- "ChEMBL-specific tool",
32
- "chembl_disease_target_score",
33
- {"efoId": "EFO_0000339"},
34
- ),
35
- ]
36
-
37
- for name, tool_name, args in tests:
38
- print(f"Testing {name}...")
39
- result = engine.run_one_function({"name": tool_name, "arguments": args})
40
- print(f"\033[92m{result}\033[0m")
41
- assert (
42
- result and result.get("total_targets_with_scores", 0) > 0
43
- ), f"{name} failed"
44
- print(f"✅ Found {result['total_targets_with_scores']} targets")
45
-
46
- print("🎉 All tests passed!")
47
- return True
48
-
49
-
50
- if __name__ == "__main__":
51
- try:
52
- test_disease_target_score_tools()
53
- print("SUCCESS")
54
- except Exception as e:
55
- print(f"FAILED: {e}")
56
- sys.exit(1)
@@ -1,179 +0,0 @@
1
- from tooluniverse import ToolUniverse
2
- from typing import Any, Dict, List
3
- import json
4
-
5
- # Initialize tool universe
6
- tooluni = ToolUniverse()
7
- tooluni.load_tools()
8
-
9
- print("=== DrugBank Filter Tool Usage Examples ===\n")
10
-
11
- # 详细的使用示例,展示如何使用各种过滤器
12
- filter_examples: List[Dict[str, Any]] = [
13
- {
14
- "name": "Example 1: Find all insulin-related drugs",
15
- "query": {
16
- "name": "drugbank_filter",
17
- "arguments": {
18
- "filters": {"Common name": {"contains": "insulin"}},
19
- "limit": 5,
20
- },
21
- },
22
- },
23
- {
24
- "name": "Example 2: Find drugs with specific DrugBank ID pattern",
25
- "query": {
26
- "name": "drugbank_filter",
27
- "arguments": {
28
- "filters": {"DrugBank ID": {"starts_with": "DB001"}},
29
- "limit": 5,
30
- },
31
- },
32
- },
33
- {
34
- "name": "Example 3: Find drugs with CAS numbers (quality check)",
35
- "query": {
36
- "name": "drugbank_filter",
37
- "arguments": {"filters": {"CAS": {"not_empty": True}}, "limit": 3},
38
- },
39
- },
40
- {
41
- "name": "Example 4: Find interferon drugs with UNII identifiers",
42
- "query": {
43
- "name": "drugbank_filter",
44
- "arguments": {
45
- "filters": {
46
- "Common name": {"contains": "interferon"},
47
- "UNII": {"not_empty": True},
48
- },
49
- "limit": 3,
50
- },
51
- },
52
- },
53
- {
54
- "name": "Example 5: Find drugs ending with 'acid'",
55
- "query": {
56
- "name": "drugbank_filter",
57
- "arguments": {
58
- "filters": {"Common name": {"ends_with": "acid"}},
59
- "limit": 4,
60
- },
61
- },
62
- },
63
- {
64
- "name": "Example 6: Simple string filter (aspirin in synonyms)",
65
- "query": {
66
- "name": "drugbank_filter",
67
- "arguments": {"filters": {"Synonyms": "aspirin"}, "limit": 3},
68
- },
69
- },
70
- {
71
- "name": "Example 7: Exact drug name match",
72
- "query": {
73
- "name": "drugbank_filter",
74
- "arguments": {
75
- "filters": {"Common name": {"exact": "Lepirudin"}},
76
- "limit": 5,
77
- },
78
- },
79
- },
80
- {
81
- "name": "Example 8: Complex multi-field filter",
82
- "query": {
83
- "name": "drugbank_filter",
84
- "arguments": {
85
- "filters": {
86
- "DrugBank ID": {"starts_with": "DB00"},
87
- "CAS": {"not_empty": True},
88
- "Common name": {"contains": "alfa"},
89
- },
90
- "limit": 3,
91
- },
92
- },
93
- },
94
- ]
95
-
96
- for idx, example in enumerate(filter_examples, 1):
97
- print(f"[{idx}] {example['name']}")
98
- print("Filter Arguments:")
99
- print(json.dumps(example["query"]["arguments"], indent=2, ensure_ascii=False))
100
-
101
- try:
102
- result = tooluni.run(example["query"])
103
-
104
- if isinstance(result, dict) and "results" in result:
105
- total = result.get("total_matches", 0)
106
- returned = result.get("returned_results", 0)
107
- print(f"✅ Success: Found {total} matches, showing {returned} results")
108
-
109
- # Show first result details
110
- if result["results"]:
111
- first = result["results"][0]
112
- print(
113
- f" First result: {first.get('Common name', 'N/A')} (ID: {first.get('DrugBank ID', 'N/A')})"
114
- )
115
- if first.get("CAS"):
116
- print(f" CAS: {first['CAS']}")
117
- if first.get("UNII"):
118
- print(f" UNII: {first['UNII']}")
119
- if first.get("Synonyms"):
120
- synonyms = (
121
- first["Synonyms"][:100] + "..."
122
- if len(first["Synonyms"]) > 100
123
- else first["Synonyms"]
124
- )
125
- print(f" Synonyms: {synonyms}")
126
-
127
- # Show applied filters
128
- if "applied_filters" in result:
129
- print(f" Applied filters: {', '.join(result['applied_filters'])}")
130
-
131
- elif isinstance(result, dict) and "error" in result:
132
- print(f"❌ Error: {result['error']}")
133
- else:
134
- print("❌ Unexpected result format")
135
-
136
- except Exception as e:
137
- print(f"❌ Exception: {e}")
138
-
139
- print("-" * 80)
140
-
141
- print("\n=== Filter Usage Summary ===")
142
- print(
143
- """
144
- Common Filter Patterns:
145
-
146
- 1. Simple String Matching:
147
- {"field_name": "search_text"}
148
-
149
- 2. Contains Pattern:
150
- {"field_name": {"contains": "text"}}
151
-
152
- 3. Starts With Pattern:
153
- {"field_name": {"starts_with": "prefix"}}
154
-
155
- 4. Ends With Pattern:
156
- {"field_name": {"ends_with": "suffix"}}
157
-
158
- 5. Exact Match:
159
- {"field_name": {"exact": "exact_value"}}
160
-
161
- 6. Data Quality Check:
162
- {"field_name": {"not_empty": true}}
163
-
164
- 7. Multiple Conditions (AND logic):
165
- {
166
- "field1": {"contains": "text1"},
167
- "field2": {"not_empty": true}
168
- }
169
-
170
- Available Fields:
171
- - DrugBank ID
172
- - Common name
173
- - CAS
174
- - UNII
175
- - Synonyms
176
- - Accession Numbers
177
- - Standard InChI Key
178
- """
179
- )
@@ -1,31 +0,0 @@
1
- from tooluniverse import ToolUniverse
2
-
3
- # Step 1: Initialize tool universe
4
- tooluni = ToolUniverse()
5
- tooluni.load_tools()
6
-
7
- # Step 2: Define test queries for the ChEMBLTool
8
- test_queries = [
9
- {
10
- "name": "OSL_get_efo_id_by_disease_name",
11
- "arguments": {"disease": "Bardet Biedl syndrome"},
12
- },
13
- {
14
- "name": "OSL_get_efo_id_by_disease_name",
15
- "arguments": {"disease": "Bardet-Biedl syndrome"},
16
- },
17
- ]
18
-
19
- # Step 3: Run all test queries
20
- for idx, query in enumerate(test_queries):
21
- # try:
22
- print(
23
- f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
24
- )
25
- result = tooluni.run(query)
26
- print("✅ Success. Example output snippet:")
27
- print(
28
- result if isinstance(result, dict) else str(result)
29
- ) # Print snippet if result is big
30
- # except Exception as e:
31
- # print(f"❌ Failed. Error: {str(e)}")
@@ -1,21 +0,0 @@
1
- from tooluniverse import ToolUniverse
2
-
3
- # Step 1: Initialize tool universe
4
- tooluni = ToolUniverse()
5
- tooluni.load_tools()
6
-
7
- #
8
- test_queries = [
9
- {
10
- "name": "enrichr_gene_enrichment_analysis",
11
- "arguments": {"gene_list": ["TP53", "USP7"]},
12
- },
13
- ]
14
-
15
- for idx, query in enumerate(test_queries):
16
- print(
17
- f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
18
- )
19
- result = tooluni.run(query)
20
- print("✅ Success. Example output snippet:")
21
- print(result if isinstance(result, dict) else str(result))
@@ -1,20 +0,0 @@
1
- from tooluniverse import ToolUniverse
2
-
3
- # ...existing code initializing ToolUniverse...
4
- tooluni = ToolUniverse()
5
- tooluni.load_tools()
6
-
7
- test_queries = [
8
- {
9
- "name": "EuropePMC_search_articles",
10
- "arguments": {"query": "cancer immunotherapy", "limit": 3},
11
- },
12
- ]
13
-
14
- for idx, query in enumerate(test_queries):
15
- print(
16
- f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
17
- )
18
- result = tooluni.run(query)
19
- print("✅ Success. Example output snippet:")
20
- print(result if isinstance(result, dict) else str(result))
@@ -1,95 +0,0 @@
1
- # === openfda_test_all_tools.py ===
2
-
3
- from tooluniverse import ToolUniverse
4
-
5
- # Step 1: Initialize tool universe
6
- tooluni = ToolUniverse()
7
- tooluni.load_tools()
8
-
9
- # Step 2: Define all test queries for all tools
10
- test_queries = [
11
- # # ====== Tests for FAERS_count_reactions_by_drug_event ======
12
- # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "LIPITOR"}},
13
- # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "LIPITOR", "patient.patientsex": "Male", "serious": "Serious"}},
14
- # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ASPIRIN", "patient.patientagegroup": "Adult"}},
15
- # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ADVIL", "patient.patientsex": "Female", "patient.patientagegroup": "Elderly", "occurcountry": "US", "serious": "Non-serious"}},
16
- # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ADVIL", "seriousnessdeath": "Yes"}},
17
- # # ====== Tests for FAERS_count_drugs_by_drug_event ======
18
- # {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"patient.patientsex": "Female"}},
19
- # {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"patient.patientagegroup": "Child"}},
20
- # {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"serious": "Serious"}},
21
- # {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"occurcountry": "CA", "serious": "Non-serious"}},
22
- # # ====== Tests for FAERS_count_country_by_drug_event ======
23
- # {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "METFORMIN"}},
24
- # {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "INSULIN", "patient.patientsex": "Male"}},
25
- # {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "ASPIRIN", "serious": "Serious"}},
26
- # {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "STATIN", "patient.patientsex": "Female", "patient.patientagegroup": "Adult", "serious": "Non-serious"}},
27
- # # ====== Tests for FAERS_count_reportercountry_by_drug_event ======
28
- # {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "LANTUS"}},
29
- # {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "AMLODIPINE", "patient.patientsex": "Unknown"}},
30
- # {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "ATORVASTATIN", "patient.patientagegroup": "Elderly"}},
31
- # {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "GABAPENTIN", "patient.patientsex": "Male", "patient.patientagegroup": "Adult", "serious": "Serious"}},
32
- # # ====== Tests for FAERS_count_seriousness_by_drug_event ======
33
- # {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "NAPROXEN"}},
34
- # {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "ALBUTEROL", "patient.patientsex": "Female"}},
35
- # {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "PREDNISONE", "patient.patientagegroup": "Child"}},
36
- # {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "METHOTREXATE", "patient.patientsex": "Male", "patient.patientagegroup": "Adult", "occurcountry": "US"}},
37
- # # ====== Tests for FAERS_count_outcomes_by_drug_event ======
38
- # {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN"}},
39
- # {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN", "patient.patientsex": "Female", "occurcountry": "GB"}},
40
- # {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN", "patient.patientsex": "Male", "patient.patientagegroup": "Adolescent"}},
41
- # # ====== Tests for FAERS_count_drug_routes_by_event ======
42
- # {"name": "FAERS_count_drug_routes_by_event", "arguments": {"medicinalproduct": "INSULIN", "serious": "Serious"}},
43
- # {"name": "FAERS_count_drug_routes_by_event", "arguments": {"medicinalproduct": "MORPHINE", "serious": "Non-serious"}},
44
- # # ====== Tests for FAERS_count_patient_age_distribution ======
45
- # {"name": "FAERS_count_patient_age_distribution", "arguments": {"medicinalproduct": "PENICILLIN"}},
46
- # {"name": "FAERS_count_patient_age_distribution", "arguments": {"medicinalproduct": "ACETAMINOPHEN"}},
47
- # ====== Tests for FAERS_count_death_related_by_drug ======
48
- # {"name": "FAERS_count_death_related_by_drug", "arguments": {"medicinalproduct": "FENTANYL"}},
49
- # {"name": "FAERS_count_death_related_by_drug", "arguments": {"medicinalproduct": "WARFARIN"}},
50
- # # ====== Tests for FAERS_count_additive_adverse_reactions ======
51
- # {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
52
- # {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "patient.patientsex": "Male"}},
53
- # {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Serious"}},
54
- # # ====== Tests for FAERS_count_additive_event_reports_by_country ======
55
- # {"name": "FAERS_count_additive_event_reports_by_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
56
- # {"name": "FAERS_count_additive_event_reports_by_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Non-serious"}},
57
- # # ====== Tests for FAERS_count_additive_reports_by_reporter_country ======
58
- # {"name": "FAERS_count_additive_reports_by_reporter_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
59
- # {"name": "FAERS_count_additive_reports_by_reporter_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "patient.patientagegroup": "Elderly"}},
60
- # # ====== Tests for FAERS_count_additive_seriousness_classification ======
61
- # {"name": "FAERS_count_additive_seriousness_classification", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
62
- # {"name": "FAERS_count_additive_seriousness_classification", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "occurcountry": "CA"}},
63
- # ====== Tests for FAERS_count_additive_reaction_outcomes ======
64
- # {"name": "FAERS_count_additive_reaction_outcomes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
65
- # {"name": "FAERS_count_additive_reaction_outcomes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
66
- # ====== Tests for FAERS_count_additive_administration_routes ======
67
- # {"name": "FAERS_count_additive_administration_routes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
68
- # {"name": "FAERS_count_additive_administration_routes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Non-serious"}},
69
- # {'name': 'FAERS_count_additive_seriousness_classification', 'arguments': {'medicinalproducts': ['Dysport'], 'occurcountry': 'US', 'patient.patientagegroup': 'Adult'}},
70
- # {'name': 'FAERS_count_additive_adverse_reactions', 'arguments': {'medicinalproducts': ['atorvastatin calcium'], 'serious': 'Yes', 'seriousnessdeath': 'Yes'}},
71
- {
72
- "name": "FAERS_count_additive_adverse_reactions",
73
- "arguments": {
74
- "medicinalproducts": ["Antara"],
75
- "patient.patientsex": "Male",
76
- "patient.patientagegroup": "Elderly",
77
- "serious": "Yes",
78
- "seriousnessdeath": "No",
79
- },
80
- },
81
- ]
82
-
83
- # Step 3: Run all test queries
84
- for idx, query in enumerate(test_queries):
85
- try:
86
- print(
87
- f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
88
- )
89
- result = tooluni.run(query)
90
- print("✅ Success. Example output snippet:")
91
- print(
92
- result if isinstance(result, dict) else str(result)[:500]
93
- ) # Print snippet if result is big
94
- except Exception as e:
95
- print(f"❌ Failed. Error: {str(e)}")