tooluniverse 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl
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- tooluniverse/__init__.py +70 -0
- tooluniverse/agentic_tool.py +121 -15
- tooluniverse/arxiv_tool.py +109 -0
- tooluniverse/base_tool.py +174 -25
- tooluniverse/biorxiv_tool.py +116 -0
- tooluniverse/cellosaurus_tool.py +1332 -0
- tooluniverse/compose_scripts/enhanced_multi_agent_literature_search.py +310 -0
- tooluniverse/compose_scripts/multi_agent_literature_search.py +794 -0
- tooluniverse/compose_scripts/tool_graph_generation.py +68 -35
- tooluniverse/compose_scripts/tool_metadata_generator.py +205 -105
- tooluniverse/compose_tool.py +93 -8
- tooluniverse/core_tool.py +155 -0
- tooluniverse/crossref_tool.py +158 -0
- tooluniverse/data/agentic_tools.json +1271 -1179
- tooluniverse/data/alphafold_tools.json +356 -105
- tooluniverse/data/arxiv_tools.json +94 -0
- tooluniverse/data/biorxiv_tools.json +75 -0
- tooluniverse/data/cellosaurus_tools.json +260 -0
- tooluniverse/data/chembl_tools.json +27 -12
- tooluniverse/data/clinicaltrials_gov_tools.json +377 -302
- tooluniverse/data/compose_tools.json +123 -16
- tooluniverse/data/core_tools.json +113 -0
- tooluniverse/data/crossref_tools.json +138 -0
- tooluniverse/data/dailymed_tools.json +17 -3
- tooluniverse/data/dataset_tools.json +1031 -588
- tooluniverse/data/dblp_tools.json +144 -0
- tooluniverse/data/disease_target_score_tools.json +20 -10
- tooluniverse/data/doaj_tools.json +140 -0
- tooluniverse/data/embedding_tools.json +362 -299
- tooluniverse/data/enrichr_tools.json +34 -27
- tooluniverse/data/europe_pmc_tools.json +108 -16
- tooluniverse/data/fatcat_tools.json +77 -0
- tooluniverse/data/fda_drug_adverse_event_tools.json +1061 -445
- tooluniverse/data/fda_drug_labeling_tools.json +6858 -6901
- tooluniverse/data/finder_tools.json +32 -37
- tooluniverse/data/gene_ontology_tools.json +19 -7
- tooluniverse/data/gwas_tools.json +1720 -959
- tooluniverse/data/hal_tools.json +75 -0
- tooluniverse/data/hpa_tools.json +53 -14
- tooluniverse/data/humanbase_tools.json +51 -43
- tooluniverse/data/idmap_tools.json +76 -70
- tooluniverse/data/literature_search_tools.json +306 -0
- tooluniverse/data/mcp_client_tools_example.json +122 -107
- tooluniverse/data/medlineplus_tools.json +50 -10
- tooluniverse/data/medrxiv_tools.json +75 -0
- tooluniverse/data/molecule_2d_tools.json +134 -0
- tooluniverse/data/molecule_3d_tools.json +164 -0
- tooluniverse/data/monarch_tools.json +112 -110
- tooluniverse/data/odphp_tools.json +389 -119
- tooluniverse/data/openaire_tools.json +95 -0
- tooluniverse/data/openalex_tools.json +100 -31
- tooluniverse/data/opentarget_tools.json +1457 -1372
- tooluniverse/data/osf_preprints_tools.json +81 -0
- tooluniverse/data/packages/bioinformatics_core_tools.json +40 -10
- tooluniverse/data/packages/cheminformatics_tools.json +20 -5
- tooluniverse/data/packages/genomics_tools.json +36 -9
- tooluniverse/data/packages/machine_learning_tools.json +36 -9
- tooluniverse/data/packages/scientific_computing_tools.json +20 -5
- tooluniverse/data/packages/single_cell_tools.json +20 -5
- tooluniverse/data/packages/structural_biology_tools.json +16 -4
- tooluniverse/data/packages/visualization_tools.json +20 -5
- tooluniverse/data/pmc_tools.json +117 -0
- tooluniverse/data/protein_structure_3d_tools.json +138 -0
- tooluniverse/data/pubchem_tools.json +37 -12
- tooluniverse/data/pubmed_tools.json +133 -0
- tooluniverse/data/pubtator_tools.json +68 -60
- tooluniverse/data/rcsb_pdb_tools.json +1532 -1221
- tooluniverse/data/semantic_scholar_tools.json +55 -22
- tooluniverse/data/special_tools.json +8 -6
- tooluniverse/data/tool_composition_tools.json +112 -82
- tooluniverse/data/unified_guideline_tools.json +707 -0
- tooluniverse/data/unpaywall_tools.json +86 -0
- tooluniverse/data/url_fetch_tools.json +102 -82
- tooluniverse/data/uspto_tools.json +49 -30
- tooluniverse/data/wikidata_sparql_tools.json +45 -0
- tooluniverse/data/xml_tools.json +3274 -3113
- tooluniverse/data/zenodo_tools.json +90 -0
- tooluniverse/dblp_tool.py +132 -0
- tooluniverse/default_config.py +30 -0
- tooluniverse/doaj_tool.py +183 -0
- tooluniverse/doctor.py +48 -0
- tooluniverse/europe_pmc_tool.py +132 -17
- tooluniverse/exceptions.py +170 -0
- tooluniverse/execute_function.py +825 -342
- tooluniverse/fatcat_tool.py +65 -0
- tooluniverse/generate_tools.py +198 -0
- tooluniverse/hal_tool.py +77 -0
- tooluniverse/llm_clients.py +283 -20
- tooluniverse/mcp_tool_registry.py +4 -1
- tooluniverse/medrxiv_tool.py +116 -0
- tooluniverse/memory_manager.py +166 -0
- tooluniverse/molecule_2d_tool.py +274 -0
- tooluniverse/molecule_3d_tool.py +441 -0
- tooluniverse/odphp_tool.py +49 -14
- tooluniverse/openaire_tool.py +130 -0
- tooluniverse/openalex_tool.py +34 -0
- tooluniverse/osf_preprints_tool.py +67 -0
- tooluniverse/pmc_tool.py +179 -0
- tooluniverse/protein_structure_3d_tool.py +295 -0
- tooluniverse/pubmed_tool.py +173 -0
- tooluniverse/remote/boltz/boltz_mcp_server.py +3 -1
- tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +3 -1
- tooluniverse/semantic_scholar_tool.py +40 -10
- tooluniverse/smcp.py +228 -263
- tooluniverse/smcp_server.py +97 -55
- tooluniverse/tool_registry.py +35 -3
- tooluniverse/tools/ADMETAI_predict_BBB_penetrance.py +46 -0
- tooluniverse/tools/ADMETAI_predict_CYP_interactions.py +46 -0
- tooluniverse/tools/ADMETAI_predict_bioavailability.py +46 -0
- tooluniverse/tools/ADMETAI_predict_clearance_distribution.py +49 -0
- tooluniverse/tools/ADMETAI_predict_nuclear_receptor_activity.py +49 -0
- tooluniverse/tools/ADMETAI_predict_physicochemical_properties.py +49 -0
- tooluniverse/tools/ADMETAI_predict_solubility_lipophilicity_hydration.py +49 -0
- tooluniverse/tools/ADMETAI_predict_stress_response.py +46 -0
- tooluniverse/tools/ADMETAI_predict_toxicity.py +46 -0
- tooluniverse/tools/AdvancedCodeQualityAnalyzer.py +63 -0
- tooluniverse/tools/AdverseEventICDMapper.py +46 -0
- tooluniverse/tools/AdverseEventPredictionQuestionGenerator.py +52 -0
- tooluniverse/tools/AdverseEventPredictionQuestionGeneratorWithContext.py +59 -0
- tooluniverse/tools/ArXiv_search_papers.py +63 -0
- tooluniverse/tools/ArgumentDescriptionOptimizer.py +55 -0
- tooluniverse/tools/BioRxiv_search_preprints.py +52 -0
- tooluniverse/tools/BiomarkerDiscoveryWorkflow.py +55 -0
- tooluniverse/tools/CORE_search_papers.py +67 -0
- tooluniverse/tools/CallAgent.py +46 -0
- tooluniverse/tools/ChEMBL_search_similar_molecules.py +59 -0
- tooluniverse/tools/CodeOptimizer.py +55 -0
- tooluniverse/tools/CodeQualityAnalyzer.py +71 -0
- tooluniverse/tools/ComprehensiveDrugDiscoveryPipeline.py +49 -0
- tooluniverse/tools/Crossref_search_works.py +55 -0
- tooluniverse/tools/DBLP_search_publications.py +52 -0
- tooluniverse/tools/DOAJ_search_articles.py +55 -0
- tooluniverse/tools/DailyMed_get_spl_by_setid.py +52 -0
- tooluniverse/tools/DailyMed_search_spls.py +79 -0
- tooluniverse/tools/DataAnalysisValidityReviewer.py +49 -0
- tooluniverse/tools/DescriptionAnalyzer.py +55 -0
- tooluniverse/tools/DescriptionQualityEvaluator.py +59 -0
- tooluniverse/tools/DomainExpertValidator.py +63 -0
- tooluniverse/tools/DrugSafetyAnalyzer.py +59 -0
- tooluniverse/tools/EthicalComplianceReviewer.py +49 -0
- tooluniverse/tools/EuropePMC_Guidelines_Search.py +52 -0
- tooluniverse/tools/EuropePMC_search_articles.py +52 -0
- tooluniverse/tools/ExperimentalDesignScorer.py +55 -0
- tooluniverse/tools/FAERS_count_additive_administration_routes.py +52 -0
- tooluniverse/tools/FAERS_count_additive_adverse_reactions.py +71 -0
- tooluniverse/tools/FAERS_count_additive_event_reports_by_country.py +63 -0
- tooluniverse/tools/FAERS_count_additive_reaction_outcomes.py +63 -0
- tooluniverse/tools/FAERS_count_additive_reports_by_reporter_country.py +63 -0
- tooluniverse/tools/FAERS_count_additive_seriousness_classification.py +63 -0
- tooluniverse/tools/FAERS_count_country_by_drug_event.py +63 -0
- tooluniverse/tools/FAERS_count_death_related_by_drug.py +49 -0
- tooluniverse/tools/FAERS_count_drug_routes_by_event.py +52 -0
- tooluniverse/tools/FAERS_count_drugs_by_drug_event.py +63 -0
- tooluniverse/tools/FAERS_count_outcomes_by_drug_event.py +63 -0
- tooluniverse/tools/FAERS_count_patient_age_distribution.py +49 -0
- tooluniverse/tools/FAERS_count_reactions_by_drug_event.py +71 -0
- tooluniverse/tools/FAERS_count_reportercountry_by_drug_event.py +63 -0
- tooluniverse/tools/FAERS_count_seriousness_by_drug_event.py +63 -0
- tooluniverse/tools/FDA_get_abuse_dependence_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_abuse_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_accessories_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_active_ingredient_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_adverse_reactions_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_alarms_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_animal_pharmacology_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_assembly_installation_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_boxed_warning_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_brand_name_generic_name.py +52 -0
- tooluniverse/tools/FDA_get_calibration_instructions_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_carcinogenic_mutagenic_fertility_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_child_safety_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_clinical_pharmacology_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_clinical_studies_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_contact_for_questions_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_contraindications_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_controlled_substance_DEA_schedule_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_dear_health_care_provider_letter_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_dependence_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_disposal_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_do_not_use_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_document_id_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_dosage_and_storage_information_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_dosage_forms_and_strengths_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_drug_generic_name.py +46 -0
- tooluniverse/tools/FDA_get_drug_interactions_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_SPL_ID.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_adverse_reaction.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_calibration_instructions.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_dependence_info.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_document_id.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_dosage_info.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_environmental_warning.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_inactive_ingredient.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_labor_and_delivery_info.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_microbiology.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_other_safety_info.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_pharmacodynamics.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_pharmacogenomics.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_precautions.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_pregnancy_or_breastfeeding_info.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_principal_display_panel.py +59 -0
- tooluniverse/tools/FDA_get_drug_name_by_reference.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_set_id.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_stop_use_info.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_storage_and_handling_info.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_by_warnings.py +55 -0
- tooluniverse/tools/FDA_get_drug_name_from_patient_package_insert.py +59 -0
- tooluniverse/tools/FDA_get_drug_names_by_abuse_dependence_info.py +55 -0
- tooluniverse/tools/FDA_get_drug_names_by_abuse_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_accessories.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_active_ingredient.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_alarm.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_animal_pharmacology_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_application_number_NDC_number.py +59 -0
- tooluniverse/tools/FDA_get_drug_names_by_assembly_installation_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_boxed_warning.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_child_safety_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_clinical_pharmacology.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_clinical_studies.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_consulting_doctor_pharmacist_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_contraindications.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_controlled_substance_DEA_schedule.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_dear_health_care_provider_letter_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_disposal_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_dosage_forms_and_strengths_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_drug_interactions.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_effective_time.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_food_safety_warnings.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_general_precautions.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_geriatric_use.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_health_claim.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_indication.py +55 -0
- tooluniverse/tools/FDA_get_drug_names_by_info_for_nursing_mothers.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_information_for_owners_or_caregivers.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_ingredient.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_instructions_for_use.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_lab_test_interference.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_lab_tests.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_mechanism_of_action.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_medication_guide.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_nonclinical_toxicology_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_nonteratogenic_effects.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_overdosage_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_pediatric_use.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_pharmacokinetics.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_population_use.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_pregnancy_effects_info.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_residue_warning.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_risk.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_route.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_safe_handling_warning.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_safety_summary.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_spl_indexing_data_elements.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_teratogenic_effects.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_user_safety_warning.py +63 -0
- tooluniverse/tools/FDA_get_drug_names_by_warnings_and_cautions.py +63 -0
- tooluniverse/tools/FDA_get_drugs_by_carcinogenic_mutagenic_fertility.py +63 -0
- tooluniverse/tools/FDA_get_effective_time_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_environmental_warning_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_general_precautions_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_geriatric_use_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_health_claims_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_inactive_ingredient_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_indications_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_info_for_nursing_mothers_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_info_for_patients_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_information_for_owners_or_caregivers_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_ingredients_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_instructions_for_use_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_lab_test_interference_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_lab_tests_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_labor_and_delivery_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_manufacturer_name_NDC_number_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_mechanism_of_action_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_medication_guide_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_microbiology_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_nonclinical_toxicology_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_nonteratogenic_effects_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_other_safety_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_overdosage_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_patient_package_insert_from_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_pediatric_use_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_pharmacodynamics_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_pharmacogenomics_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_pharmacokinetics_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_population_use_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_precautions_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_pregnancy_effects_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_pregnancy_or_breastfeeding_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_principal_display_panel_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_purpose_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_recent_changes_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_reference_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_residue_warning_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_risk_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_route_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_safe_handling_warnings_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_safety_summary_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_spl_indexing_data_elements_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_spl_unclassified_section_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_stop_use_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_storage_and_handling_info_by_drug_name.py +55 -0
- tooluniverse/tools/FDA_get_teratogenic_effects_by_drug_name.py +55 -0
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- tooluniverse/tools/get_mudata_info.py +49 -0
- tooluniverse/tools/get_mutation_annotations_by_pdb_id.py +46 -0
- tooluniverse/tools/get_neo_info.py +44 -0
- tooluniverse/tools/get_netcdf4_info.py +44 -0
- tooluniverse/tools/get_networkx_info.py +46 -0
- tooluniverse/tools/get_nglview_info.py +44 -0
- tooluniverse/tools/get_nilearn_info.py +44 -0
- tooluniverse/tools/get_numba_info.py +46 -0
- tooluniverse/tools/get_numpy_info.py +46 -0
- tooluniverse/tools/get_oligosaccharide_descriptors_by_entity_id.py +49 -0
- tooluniverse/tools/get_openbabel_info.py +49 -0
- tooluniverse/tools/get_openchem_info.py +46 -0
- tooluniverse/tools/get_opencv_info.py +49 -0
- tooluniverse/tools/get_openmm_info.py +49 -0
- tooluniverse/tools/get_optlang_info.py +46 -0
- tooluniverse/tools/get_optuna_info.py +44 -0
- tooluniverse/tools/get_palantir_info.py +44 -0
- tooluniverse/tools/get_pandas_info.py +49 -0
- tooluniverse/tools/get_patsy_info.py +44 -0
- tooluniverse/tools/get_pdbfixer_info.py +46 -0
- tooluniverse/tools/get_phenotype_by_HPO_ID.py +46 -0
- tooluniverse/tools/get_pillow_info.py +44 -0
- tooluniverse/tools/get_plantcv_info.py +46 -0
- tooluniverse/tools/get_plip_info.py +46 -0
- tooluniverse/tools/get_plotly_info.py +44 -0
- tooluniverse/tools/get_poliastro_info.py +46 -0
- tooluniverse/tools/get_polymer_entity_annotations.py +49 -0
- tooluniverse/tools/get_polymer_entity_count_by_pdb_id.py +46 -0
- tooluniverse/tools/get_polymer_entity_ids_by_pdb_id.py +46 -0
- tooluniverse/tools/get_polymer_entity_type_by_entity_id.py +49 -0
- tooluniverse/tools/get_polymer_molecular_weight_by_entity_id.py +49 -0
- tooluniverse/tools/get_poretools_info.py +44 -0
- tooluniverse/tools/get_prody_info.py +46 -0
- tooluniverse/tools/get_protein_classification_by_pdb_id.py +49 -0
- tooluniverse/tools/get_protein_metadata_by_pdb_id.py +46 -0
- tooluniverse/tools/get_pubchempy_info.py +44 -0
- tooluniverse/tools/get_pybedtools_info.py +49 -0
- tooluniverse/tools/get_pybigwig_info.py +46 -0
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- tooluniverse/tools/get_pyensembl_info.py +44 -0
- tooluniverse/tools/get_pyephem_info.py +44 -0
- tooluniverse/tools/get_pyfaidx_info.py +49 -0
- tooluniverse/tools/get_pyfasta_info.py +44 -0
- tooluniverse/tools/get_pykalman_info.py +46 -0
- tooluniverse/tools/get_pyliftover_info.py +49 -0
- tooluniverse/tools/get_pymassspec_info.py +46 -0
- tooluniverse/tools/get_pymed_info.py +46 -0
- tooluniverse/tools/get_pymzml_info.py +46 -0
- tooluniverse/tools/get_pypdf2_info.py +46 -0
- tooluniverse/tools/get_pyranges_info.py +49 -0
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- tooluniverse/tools/get_pyscenic_info.py +46 -0
- tooluniverse/tools/get_pyscf_info.py +46 -0
- tooluniverse/tools/get_pyscreener_info.py +46 -0
- tooluniverse/tools/get_pytdc_info.py +46 -0
- tooluniverse/tools/get_python_libsbml_info.py +46 -0
- tooluniverse/tools/get_pytorch_info.py +49 -0
- tooluniverse/tools/get_pyvcf_info.py +44 -0
- tooluniverse/tools/get_pyvis_info.py +44 -0
- tooluniverse/tools/get_qutip_info.py +44 -0
- tooluniverse/tools/get_rasterio_info.py +44 -0
- tooluniverse/tools/get_rdkit_info.py +46 -0
- tooluniverse/tools/get_refinement_resolution_by_pdb_id.py +49 -0
- tooluniverse/tools/get_release_deposit_dates_by_pdb_id.py +49 -0
- tooluniverse/tools/get_reportlab_info.py +49 -0
- tooluniverse/tools/get_requests_info.py +49 -0
- tooluniverse/tools/get_ruptures_info.py +46 -0
- tooluniverse/tools/get_scanorama_info.py +44 -0
- tooluniverse/tools/get_scanpy_info.py +49 -0
- tooluniverse/tools/get_schnetpack_info.py +49 -0
- tooluniverse/tools/get_scholarly_info.py +46 -0
- tooluniverse/tools/get_scikit_bio_info.py +49 -0
- tooluniverse/tools/get_scikit_image_info.py +46 -0
- tooluniverse/tools/get_scikit_learn_info.py +49 -0
- tooluniverse/tools/get_scipy_info.py +46 -0
- tooluniverse/tools/get_scrublet_info.py +49 -0
- tooluniverse/tools/get_scvelo_info.py +49 -0
- tooluniverse/tools/get_scvi_tools_info.py +44 -0
- tooluniverse/tools/get_seaborn_info.py +49 -0
- tooluniverse/tools/get_sequence_by_pdb_id.py +46 -0
- tooluniverse/tools/get_sequence_lengths_by_pdb_id.py +46 -0
- tooluniverse/tools/get_sequence_positional_features_by_instance_id.py +49 -0
- tooluniverse/tools/get_skopt_info.py +44 -0
- tooluniverse/tools/get_souporcell_info.py +46 -0
- tooluniverse/tools/get_source_organism_by_pdb_id.py +46 -0
- tooluniverse/tools/get_space_group_by_pdb_id.py +46 -0
- tooluniverse/tools/get_statsmodels_info.py +49 -0
- tooluniverse/tools/get_structure_determination_software_by_pdb_id.py +49 -0
- tooluniverse/tools/get_structure_title_by_pdb_id.py +46 -0
- tooluniverse/tools/get_structure_validation_metrics_by_pdb_id.py +49 -0
- tooluniverse/tools/get_sunpy_info.py +44 -0
- tooluniverse/tools/get_sympy_info.py +46 -0
- tooluniverse/tools/get_target_cofactor_info.py +46 -0
- tooluniverse/tools/get_taxonomy_by_pdb_id.py +46 -0
- tooluniverse/tools/get_tiledb_info.py +46 -0
- tooluniverse/tools/get_tiledbsoma_info.py +46 -0
- tooluniverse/tools/get_torch_geometric_info.py +49 -0
- tooluniverse/tools/get_tqdm_info.py +46 -0
- tooluniverse/tools/get_trackpy_info.py +46 -0
- tooluniverse/tools/get_tskit_info.py +46 -0
- tooluniverse/tools/get_umap_learn_info.py +49 -0
- tooluniverse/tools/get_uniprot_accession_by_entity_id.py +49 -0
- tooluniverse/tools/get_velocyto_info.py +44 -0
- tooluniverse/tools/get_viennarna_info.py +49 -0
- tooluniverse/tools/get_webpage_text_from_url.py +52 -0
- tooluniverse/tools/get_webpage_title.py +49 -0
- tooluniverse/tools/get_xarray_info.py +44 -0
- tooluniverse/tools/get_xesmf_info.py +44 -0
- tooluniverse/tools/get_xgboost_info.py +44 -0
- tooluniverse/tools/get_zarr_info.py +44 -0
- tooluniverse/tools/gwas_get_association_by_id.py +49 -0
- tooluniverse/tools/gwas_get_associations_for_snp.py +67 -0
- tooluniverse/tools/gwas_get_associations_for_study.py +55 -0
- tooluniverse/tools/gwas_get_associations_for_trait.py +55 -0
- tooluniverse/tools/gwas_get_snp_by_id.py +46 -0
- tooluniverse/tools/gwas_get_snps_for_gene.py +55 -0
- tooluniverse/tools/gwas_get_studies_for_trait.py +75 -0
- tooluniverse/tools/gwas_get_study_by_id.py +46 -0
- tooluniverse/tools/gwas_get_variants_for_trait.py +55 -0
- tooluniverse/tools/gwas_search_associations.py +75 -0
- tooluniverse/tools/gwas_search_snps.py +63 -0
- tooluniverse/tools/gwas_search_studies.py +75 -0
- tooluniverse/tools/humanbase_ppi_analysis.py +67 -0
- tooluniverse/tools/mesh_get_subjects_by_pharmacological_action.py +63 -0
- tooluniverse/tools/mesh_get_subjects_by_subject_id.py +63 -0
- tooluniverse/tools/mesh_get_subjects_by_subject_name.py +63 -0
- tooluniverse/tools/mesh_get_subjects_by_subject_scope_or_definition.py +63 -0
- tooluniverse/tools/odphp_itemlist.py +49 -0
- tooluniverse/tools/odphp_myhealthfinder.py +67 -0
- tooluniverse/tools/odphp_outlink_fetch.py +59 -0
- tooluniverse/tools/odphp_topicsearch.py +67 -0
- tooluniverse/tools/openalex_literature_search.py +67 -0
- tooluniverse/tools/reactome_disease_target_score.py +52 -0
- tooluniverse/tools/search_clinical_trials.py +67 -0
- tooluniverse/tools/visualize_molecule_2d.py +83 -0
- tooluniverse/tools/visualize_molecule_3d.py +91 -0
- tooluniverse/tools/visualize_protein_structure_3d.py +79 -0
- tooluniverse/unified_guideline_tools.py +1210 -0
- tooluniverse/unpaywall_tool.py +62 -0
- tooluniverse/utils.py +71 -2
- tooluniverse/visualization_tool.py +897 -0
- tooluniverse/wikidata_sparql_tool.py +60 -0
- tooluniverse/zenodo_tool.py +72 -0
- {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/METADATA +12 -2
- tooluniverse-1.0.7.dist-info/RECORD +855 -0
- {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/entry_points.txt +4 -0
- tooluniverse/test/list_azure_openai_models.py +0 -210
- tooluniverse/test/mcp_server_test.py +0 -0
- tooluniverse/test/test_admetai_tool.py +0 -370
- tooluniverse/test/test_agentic_tool.py +0 -129
- tooluniverse/test/test_agentic_tool_azure_models.py +0 -91
- tooluniverse/test/test_alphafold_tool.py +0 -108
- tooluniverse/test/test_api_key_validation_min.py +0 -64
- tooluniverse/test/test_chem_tool.py +0 -37
- tooluniverse/test/test_claude_sdk.py +0 -86
- tooluniverse/test/test_compose_lieraturereview.py +0 -63
- tooluniverse/test/test_compose_tool.py +0 -448
- tooluniverse/test/test_dailymed.py +0 -69
- tooluniverse/test/test_dataset_tool.py +0 -200
- tooluniverse/test/test_disease_target_score.py +0 -56
- tooluniverse/test/test_drugbank_filter_examples.py +0 -179
- tooluniverse/test/test_efo.py +0 -31
- tooluniverse/test/test_enrichr_tool.py +0 -21
- tooluniverse/test/test_europe_pmc_tool.py +0 -20
- tooluniverse/test/test_fda_adv.py +0 -95
- tooluniverse/test/test_fda_drug_labeling.py +0 -91
- tooluniverse/test/test_gene_ontology_tools.py +0 -66
- tooluniverse/test/test_global_fallback.py +0 -288
- tooluniverse/test/test_gwas_tool.py +0 -139
- tooluniverse/test/test_hooks_direct.py +0 -219
- tooluniverse/test/test_hpa.py +0 -625
- tooluniverse/test/test_humanbase_tool.py +0 -20
- tooluniverse/test/test_idmap_tools.py +0 -61
- tooluniverse/test/test_list_built_in_tools.py +0 -33
- tooluniverse/test/test_mcp_server.py +0 -211
- tooluniverse/test/test_mcp_tool.py +0 -247
- tooluniverse/test/test_medlineplus.py +0 -220
- tooluniverse/test/test_odphp_tool.py +0 -166
- tooluniverse/test/test_openalex_tool.py +0 -32
- tooluniverse/test/test_openrouter_client.py +0 -288
- tooluniverse/test/test_opentargets.py +0 -28
- tooluniverse/test/test_pubchem_tool.py +0 -116
- tooluniverse/test/test_pubtator_tool.py +0 -37
- tooluniverse/test/test_rcsb_pdb_tool.py +0 -86
- tooluniverse/test/test_reactome.py +0 -54
- tooluniverse/test/test_semantic_scholar_tool.py +0 -24
- tooluniverse/test/test_software_tools.py +0 -147
- tooluniverse/test/test_stdio_hooks.py +0 -285
- tooluniverse/test/test_tool_description_optimizer.py +0 -49
- tooluniverse/test/test_tool_finder.py +0 -26
- tooluniverse/test/test_tool_finder_llm.py +0 -252
- tooluniverse/test/test_tools_find.py +0 -195
- tooluniverse/test/test_uniprot_tools.py +0 -74
- tooluniverse/test/test_uspto_tool.py +0 -72
- tooluniverse/test/test_xml_tool.py +0 -113
- tooluniverse-1.0.5.dist-info/RECORD +0 -198
- {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/WHEEL +0 -0
- {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/licenses/LICENSE +0 -0
- {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/top_level.txt +0 -0
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from tooluniverse import ToolUniverse
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# Step 1: Initialize tool universe
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tooluni = ToolUniverse()
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tooluni.load_tools()
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test_queries = [
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# Test 1: Search for a specific drug by name
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{"name": "drugbank_vocab_search", "arguments": {"query": "aspirin"}},
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# Test 2: Exact match search for a DrugBank ID
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{
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"name": "drugbank_vocab_search",
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"arguments": {
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"query": "DB00001",
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"search_fields": ["DrugBank ID"],
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"exact_match": True,
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},
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},
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# Test 3: Search in synonyms with case sensitivity
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{
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"name": "drugbank_vocab_search",
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"arguments": {
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"query": "Lepirudin",
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"search_fields": ["Synonyms", "Common name"],
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"case_sensitive": True,
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"limit": 10,
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},
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# Test 4: Filter drugs that have CAS numbers
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{
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"name": "drugbank_vocab_filter",
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"arguments": {"field": "CAS", "condition": "not_empty", "limit": 5},
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},
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# Test 5: Filter drugs starting with "DB000"
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{
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"name": "drugbank_vocab_filter",
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"arguments": {
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"field": "DrugBank ID",
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"condition": "starts_with",
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"value": "DB000",
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"limit": 10,
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},
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# Test 6: Filter drugs containing "interferon" in common name
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{
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"name": "drugbank_vocab_filter",
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"arguments": {
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"field": "Common name",
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"condition": "contains",
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"value": "interferon",
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"limit": 5,
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# Test 7: Complex search with multiple fields
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"name": "drugbank_vocab_search",
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"arguments": {
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"query": "insulin",
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"search_fields": ["Common name", "Synonyms"],
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"case_sensitive": False,
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# ---------- drugbank_full_search ----------
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# 1. Partial common-name query
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"name": "drugbank_full_search",
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"arguments": {
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"query": "acetylsalicylic",
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"search_fields": ["name"],
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# 2. Exact-match lookup by DrugBank ID
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"name": "drugbank_full_search",
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"arguments": {
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"query": "DB00003",
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"search_fields": ["drugbank_id"],
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# 3. Case-sensitive synonym search
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"name": "drugbank_full_search",
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"arguments": {
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"query": "Olanzapine",
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"search_fields": ["synonyms"],
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# ---------- drugbank_links_search ----------
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# 4. Exact CAS-number lookup
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"name": "drugbank_links_search",
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"arguments": {
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"query": "205923-56-4",
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"search_fields": ["CAS Number"],
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"exact_match": True,
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# 5. Search by PharmGKB identifier
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"name": "drugbank_links_search",
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"arguments": {"query": "PA10040", "search_fields": ["PharmGKB ID"]},
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# 6. Search by KEGG Drug ID
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"name": "drugbank_links_search",
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"arguments": {"query": "D03455", "search_fields": ["KEGG Drug ID"]},
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},
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# ---------- dict_search (DICTrank) ----------
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# 7. Search by trade name
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"name": "dict_search",
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"arguments": {"query": "ZYPREXA", "search_fields": ["Trade Name"], "limit": 2},
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# 8. Search by active ingredient (case-insensitive)
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"name": "dict_search",
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"arguments": {
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"query": "trimethobenzamide",
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"search_fields": ["Active Ingredient(s)"],
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# ---------- dili_search (DILIrank) ----------
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# 9. Exact compound-name search
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"name": "dili_search",
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"arguments": {
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"query": "acetaminophen",
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"search_fields": ["Compound Name"],
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# 10. Partial compound-name query
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"name": "dili_search",
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"arguments": {
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"query": "mercap",
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"search_fields": ["Compound Name"],
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# ---------- diqt_search (DIQTA) ----------
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# 11. Exact DrugBank ID lookup
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{
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"name": "diqt_search",
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"arguments": {
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"query": "DB00637",
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"search_fields": ["DrugBank ID"],
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"exact_match": True,
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},
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},
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# 12. Generic name search (case-insensitive)
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{
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"search_fields": ["Generic/Proper Name(s)"],
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]
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for idx, query in enumerate(test_queries):
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print(
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f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
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)
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try:
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result = tooluni.run(query)
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print("✅ Success. Example output snippet:")
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if "results" in result:
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print(
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)
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if result["results"]:
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first_result = result["results"][0]
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# print(f"First result: {first_result.get('Common name', 'N/A')} (ID: {first_result.get('DrugBank ID', 'N/A')})")
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print(f"First result: {first_result})")
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if "matched_fields" in first_result:
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print(f"Matched fields: {first_result['matched_fields']}")
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elif "error" in result:
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print(f"Error: {result['error']}")
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else:
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print(
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)
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else:
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print(str(result)[:200] + "..." if len(str(result)) > 200 else str(result))
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except Exception as e:
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print(f"❌ Error: {e}")
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@@ -1,56 +0,0 @@
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#!/usr/bin/env python3
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"""
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Simple test for disease-target score extraction tools.
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"""
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import sys
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import os
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# Add the src directory to the path
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sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", "src"))
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from tooluniverse import ToolUniverse # noqa: E402
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def test_disease_target_score_tools():
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"""Test the disease-target score extraction tools"""
|
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print("Testing Disease-Target Score Tools...")
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|
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|
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# Initialize ToolUniverse and load all tools
|
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engine = ToolUniverse()
|
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engine.load_tools()
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|
|
23
|
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# Test both generic and specific tools
|
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tests = [
|
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(
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"generic tool",
|
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"disease_target_score",
|
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|
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{"efoId": "EFO_0000339", "datasourceId": "impc"},
|
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),
|
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|
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(
|
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"ChEMBL-specific tool",
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|
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"chembl_disease_target_score",
|
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33
|
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{"efoId": "EFO_0000339"},
|
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|
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),
|
|
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|
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]
|
|
36
|
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|
|
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
|
-
)
|
tooluniverse/test/test_efo.py
DELETED
|
@@ -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))
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from tooluniverse import ToolUniverse
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# ...existing code initializing ToolUniverse...
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tooluni = ToolUniverse()
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tooluni.load_tools()
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test_queries = [
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{
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"name": "EuropePMC_search_articles",
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"arguments": {"query": "cancer immunotherapy", "limit": 3},
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},
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]
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for idx, query in enumerate(test_queries):
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print(
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f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
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)
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result = tooluni.run(query)
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print("✅ Success. Example output snippet:")
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print(result if isinstance(result, dict) else str(result))
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# === openfda_test_all_tools.py ===
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from tooluniverse import ToolUniverse
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# Step 1: Initialize tool universe
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tooluni = ToolUniverse()
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tooluni.load_tools()
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# Step 2: Define all test queries for all tools
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test_queries = [
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# # ====== Tests for FAERS_count_reactions_by_drug_event ======
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# {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "LIPITOR"}},
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# {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "LIPITOR", "patient.patientsex": "Male", "serious": "Serious"}},
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# {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ASPIRIN", "patient.patientagegroup": "Adult"}},
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# {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ADVIL", "patient.patientsex": "Female", "patient.patientagegroup": "Elderly", "occurcountry": "US", "serious": "Non-serious"}},
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# {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ADVIL", "seriousnessdeath": "Yes"}},
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# # ====== Tests for FAERS_count_drugs_by_drug_event ======
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# {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"patient.patientsex": "Female"}},
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# {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"patient.patientagegroup": "Child"}},
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# {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"serious": "Serious"}},
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# {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"occurcountry": "CA", "serious": "Non-serious"}},
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# # ====== Tests for FAERS_count_country_by_drug_event ======
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# {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "METFORMIN"}},
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# {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "INSULIN", "patient.patientsex": "Male"}},
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# {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "ASPIRIN", "serious": "Serious"}},
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# {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "STATIN", "patient.patientsex": "Female", "patient.patientagegroup": "Adult", "serious": "Non-serious"}},
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# # ====== Tests for FAERS_count_reportercountry_by_drug_event ======
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# {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "LANTUS"}},
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# {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "AMLODIPINE", "patient.patientsex": "Unknown"}},
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# {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "ATORVASTATIN", "patient.patientagegroup": "Elderly"}},
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# {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "GABAPENTIN", "patient.patientsex": "Male", "patient.patientagegroup": "Adult", "serious": "Serious"}},
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# # ====== Tests for FAERS_count_seriousness_by_drug_event ======
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# {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "NAPROXEN"}},
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# {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "ALBUTEROL", "patient.patientsex": "Female"}},
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# {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "PREDNISONE", "patient.patientagegroup": "Child"}},
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# {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "METHOTREXATE", "patient.patientsex": "Male", "patient.patientagegroup": "Adult", "occurcountry": "US"}},
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# # ====== Tests for FAERS_count_outcomes_by_drug_event ======
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# {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN"}},
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# {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN", "patient.patientsex": "Female", "occurcountry": "GB"}},
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# {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN", "patient.patientsex": "Male", "patient.patientagegroup": "Adolescent"}},
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# # ====== Tests for FAERS_count_drug_routes_by_event ======
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# {"name": "FAERS_count_drug_routes_by_event", "arguments": {"medicinalproduct": "INSULIN", "serious": "Serious"}},
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# {"name": "FAERS_count_drug_routes_by_event", "arguments": {"medicinalproduct": "MORPHINE", "serious": "Non-serious"}},
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# # ====== Tests for FAERS_count_patient_age_distribution ======
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# {"name": "FAERS_count_patient_age_distribution", "arguments": {"medicinalproduct": "PENICILLIN"}},
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# {"name": "FAERS_count_patient_age_distribution", "arguments": {"medicinalproduct": "ACETAMINOPHEN"}},
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# ====== Tests for FAERS_count_death_related_by_drug ======
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# {"name": "FAERS_count_death_related_by_drug", "arguments": {"medicinalproduct": "FENTANYL"}},
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# {"name": "FAERS_count_death_related_by_drug", "arguments": {"medicinalproduct": "WARFARIN"}},
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# # ====== Tests for FAERS_count_additive_adverse_reactions ======
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# {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
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# {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "patient.patientsex": "Male"}},
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# {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Serious"}},
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# # ====== Tests for FAERS_count_additive_event_reports_by_country ======
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# {"name": "FAERS_count_additive_event_reports_by_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
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# {"name": "FAERS_count_additive_event_reports_by_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Non-serious"}},
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# # ====== Tests for FAERS_count_additive_reports_by_reporter_country ======
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# {"name": "FAERS_count_additive_reports_by_reporter_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
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# {"name": "FAERS_count_additive_reports_by_reporter_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "patient.patientagegroup": "Elderly"}},
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# # ====== Tests for FAERS_count_additive_seriousness_classification ======
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# {"name": "FAERS_count_additive_seriousness_classification", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
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# {"name": "FAERS_count_additive_seriousness_classification", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "occurcountry": "CA"}},
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# ====== Tests for FAERS_count_additive_reaction_outcomes ======
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# {"name": "FAERS_count_additive_reaction_outcomes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
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# {"name": "FAERS_count_additive_reaction_outcomes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
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# ====== Tests for FAERS_count_additive_administration_routes ======
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# {"name": "FAERS_count_additive_administration_routes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
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# {"name": "FAERS_count_additive_administration_routes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Non-serious"}},
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# {'name': 'FAERS_count_additive_seriousness_classification', 'arguments': {'medicinalproducts': ['Dysport'], 'occurcountry': 'US', 'patient.patientagegroup': 'Adult'}},
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# {'name': 'FAERS_count_additive_adverse_reactions', 'arguments': {'medicinalproducts': ['atorvastatin calcium'], 'serious': 'Yes', 'seriousnessdeath': 'Yes'}},
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{
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"name": "FAERS_count_additive_adverse_reactions",
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"arguments": {
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"medicinalproducts": ["Antara"],
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"patient.patientsex": "Male",
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"patient.patientagegroup": "Elderly",
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"serious": "Yes",
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"seriousnessdeath": "No",
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},
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},
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]
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82
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83
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# Step 3: Run all test queries
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84
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for idx, query in enumerate(test_queries):
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85
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try:
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86
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print(
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87
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f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
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88
|
-
)
|
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89
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-
result = tooluni.run(query)
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90
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-
print("✅ Success. Example output snippet:")
|
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91
|
-
print(
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92
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result if isinstance(result, dict) else str(result)[:500]
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93
|
-
) # Print snippet if result is big
|
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94
|
-
except Exception as e:
|
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95
|
-
print(f"❌ Failed. Error: {str(e)}")
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