tooluniverse 1.0.9.1__py3-none-any.whl → 1.0.11__py3-none-any.whl

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Files changed (191) hide show
  1. tooluniverse/__init__.py +57 -1
  2. tooluniverse/admetai_tool.py +1 -1
  3. tooluniverse/agentic_tool.py +65 -17
  4. tooluniverse/base_tool.py +19 -8
  5. tooluniverse/blast_tool.py +132 -0
  6. tooluniverse/boltz_tool.py +3 -3
  7. tooluniverse/cache/result_cache_manager.py +167 -12
  8. tooluniverse/cbioportal_tool.py +42 -0
  9. tooluniverse/clinvar_tool.py +268 -74
  10. tooluniverse/compose_scripts/drug_safety_analyzer.py +1 -1
  11. tooluniverse/compose_scripts/multi_agent_literature_search.py +1 -1
  12. tooluniverse/compose_scripts/output_summarizer.py +4 -4
  13. tooluniverse/compose_scripts/tool_discover.py +1941 -443
  14. tooluniverse/compose_scripts/tool_graph_composer.py +1 -1
  15. tooluniverse/compose_scripts/tool_metadata_generator.py +1 -1
  16. tooluniverse/compose_tool.py +9 -9
  17. tooluniverse/core_tool.py +2 -2
  18. tooluniverse/ctg_tool.py +4 -4
  19. tooluniverse/custom_tool.py +1 -1
  20. tooluniverse/data/agentic_tools.json +0 -370
  21. tooluniverse/data/alphafold_tools.json +6 -6
  22. tooluniverse/data/blast_tools.json +112 -0
  23. tooluniverse/data/cbioportal_tools.json +87 -0
  24. tooluniverse/data/clinvar_tools.json +235 -0
  25. tooluniverse/data/compose_tools.json +0 -89
  26. tooluniverse/data/dbsnp_tools.json +275 -0
  27. tooluniverse/data/emdb_tools.json +61 -0
  28. tooluniverse/data/ensembl_tools.json +259 -0
  29. tooluniverse/data/file_download_tools.json +275 -0
  30. tooluniverse/data/geo_tools.json +200 -48
  31. tooluniverse/data/gnomad_tools.json +109 -0
  32. tooluniverse/data/gtopdb_tools.json +68 -0
  33. tooluniverse/data/gwas_tools.json +32 -0
  34. tooluniverse/data/interpro_tools.json +199 -0
  35. tooluniverse/data/jaspar_tools.json +70 -0
  36. tooluniverse/data/kegg_tools.json +356 -0
  37. tooluniverse/data/mpd_tools.json +87 -0
  38. tooluniverse/data/ols_tools.json +314 -0
  39. tooluniverse/data/package_discovery_tools.json +64 -0
  40. tooluniverse/data/packages/categorized_tools.txt +0 -1
  41. tooluniverse/data/packages/machine_learning_tools.json +0 -47
  42. tooluniverse/data/paleobiology_tools.json +91 -0
  43. tooluniverse/data/pride_tools.json +62 -0
  44. tooluniverse/data/pypi_package_inspector_tools.json +158 -0
  45. tooluniverse/data/python_executor_tools.json +341 -0
  46. tooluniverse/data/regulomedb_tools.json +50 -0
  47. tooluniverse/data/remap_tools.json +89 -0
  48. tooluniverse/data/screen_tools.json +89 -0
  49. tooluniverse/data/tool_discovery_agents.json +428 -0
  50. tooluniverse/data/tool_discovery_agents.json.backup +1343 -0
  51. tooluniverse/data/uniprot_tools.json +77 -0
  52. tooluniverse/data/web_search_tools.json +250 -0
  53. tooluniverse/data/worms_tools.json +55 -0
  54. tooluniverse/dataset_tool.py +2 -2
  55. tooluniverse/dbsnp_tool.py +196 -58
  56. tooluniverse/default_config.py +36 -3
  57. tooluniverse/emdb_tool.py +30 -0
  58. tooluniverse/enrichr_tool.py +14 -14
  59. tooluniverse/ensembl_tool.py +140 -47
  60. tooluniverse/execute_function.py +594 -29
  61. tooluniverse/extended_hooks.py +4 -4
  62. tooluniverse/file_download_tool.py +269 -0
  63. tooluniverse/gene_ontology_tool.py +1 -1
  64. tooluniverse/generate_tools.py +3 -3
  65. tooluniverse/geo_tool.py +81 -28
  66. tooluniverse/gnomad_tool.py +100 -52
  67. tooluniverse/gtopdb_tool.py +41 -0
  68. tooluniverse/humanbase_tool.py +10 -10
  69. tooluniverse/interpro_tool.py +72 -0
  70. tooluniverse/jaspar_tool.py +30 -0
  71. tooluniverse/kegg_tool.py +230 -0
  72. tooluniverse/logging_config.py +2 -2
  73. tooluniverse/mcp_client_tool.py +57 -129
  74. tooluniverse/mcp_integration.py +52 -49
  75. tooluniverse/mcp_tool_registry.py +147 -528
  76. tooluniverse/mpd_tool.py +42 -0
  77. tooluniverse/ncbi_eutils_tool.py +96 -0
  78. tooluniverse/ols_tool.py +435 -0
  79. tooluniverse/openalex_tool.py +8 -8
  80. tooluniverse/openfda_tool.py +2 -2
  81. tooluniverse/output_hook.py +15 -15
  82. tooluniverse/package_discovery_tool.py +217 -0
  83. tooluniverse/package_tool.py +1 -1
  84. tooluniverse/paleobiology_tool.py +30 -0
  85. tooluniverse/pmc_tool.py +2 -2
  86. tooluniverse/pride_tool.py +30 -0
  87. tooluniverse/pypi_package_inspector_tool.py +593 -0
  88. tooluniverse/python_executor_tool.py +711 -0
  89. tooluniverse/regulomedb_tool.py +30 -0
  90. tooluniverse/remap_tool.py +44 -0
  91. tooluniverse/remote/boltz/boltz_mcp_server.py +1 -1
  92. tooluniverse/remote/depmap_24q2/depmap_24q2_mcp_tool.py +3 -3
  93. tooluniverse/remote/immune_compass/compass_tool.py +3 -3
  94. tooluniverse/remote/pinnacle/pinnacle_tool.py +2 -2
  95. tooluniverse/remote/transcriptformer/transcriptformer_tool.py +3 -3
  96. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +3 -3
  97. tooluniverse/remote_tool.py +4 -4
  98. tooluniverse/screen_tool.py +44 -0
  99. tooluniverse/scripts/filter_tool_files.py +2 -2
  100. tooluniverse/smcp.py +93 -12
  101. tooluniverse/smcp_server.py +100 -21
  102. tooluniverse/space/__init__.py +46 -0
  103. tooluniverse/space/loader.py +133 -0
  104. tooluniverse/space/validator.py +353 -0
  105. tooluniverse/tool_finder_embedding.py +5 -3
  106. tooluniverse/tool_finder_keyword.py +12 -10
  107. tooluniverse/tool_finder_llm.py +12 -8
  108. tooluniverse/tools/{UCSC_get_genes_by_region.py → BLAST_nucleotide_search.py} +22 -26
  109. tooluniverse/tools/BLAST_protein_search.py +63 -0
  110. tooluniverse/tools/ClinVar_search_variants.py +26 -15
  111. tooluniverse/tools/CodeQualityAnalyzer.py +3 -3
  112. tooluniverse/tools/EMDB_get_structure.py +46 -0
  113. tooluniverse/tools/GtoPdb_get_targets.py +52 -0
  114. tooluniverse/tools/InterPro_get_domain_details.py +46 -0
  115. tooluniverse/tools/InterPro_get_protein_domains.py +49 -0
  116. tooluniverse/tools/InterPro_search_domains.py +52 -0
  117. tooluniverse/tools/JASPAR_get_transcription_factors.py +52 -0
  118. tooluniverse/tools/MPD_get_phenotype_data.py +59 -0
  119. tooluniverse/tools/PRIDE_search_proteomics.py +52 -0
  120. tooluniverse/tools/PackageAnalyzer.py +55 -0
  121. tooluniverse/tools/Paleobiology_get_fossils.py +52 -0
  122. tooluniverse/tools/PyPIPackageInspector.py +59 -0
  123. tooluniverse/tools/ReMap_get_transcription_factor_binding.py +59 -0
  124. tooluniverse/tools/ReferenceInfoAnalyzer.py +55 -0
  125. tooluniverse/tools/RegulomeDB_query_variant.py +46 -0
  126. tooluniverse/tools/SCREEN_get_regulatory_elements.py +59 -0
  127. tooluniverse/tools/{ArgumentDescriptionOptimizer.py → TestResultsAnalyzer.py} +13 -13
  128. tooluniverse/tools/ToolDiscover.py +11 -11
  129. tooluniverse/tools/UniProt_id_mapping.py +63 -0
  130. tooluniverse/tools/UniProt_search.py +63 -0
  131. tooluniverse/tools/UnifiedToolGenerator.py +59 -0
  132. tooluniverse/tools/WoRMS_search_species.py +49 -0
  133. tooluniverse/tools/XMLToolOptimizer.py +55 -0
  134. tooluniverse/tools/__init__.py +119 -29
  135. tooluniverse/tools/_shared_client.py +3 -3
  136. tooluniverse/tools/alphafold_get_annotations.py +3 -3
  137. tooluniverse/tools/alphafold_get_prediction.py +3 -3
  138. tooluniverse/tools/alphafold_get_summary.py +3 -3
  139. tooluniverse/tools/cBioPortal_get_cancer_studies.py +46 -0
  140. tooluniverse/tools/cBioPortal_get_mutations.py +52 -0
  141. tooluniverse/tools/{gnomAD_query_variant.py → clinvar_get_clinical_significance.py} +8 -11
  142. tooluniverse/tools/clinvar_get_variant_details.py +49 -0
  143. tooluniverse/tools/dbSNP_get_variant_by_rsid.py +7 -7
  144. tooluniverse/tools/dbsnp_get_frequencies.py +46 -0
  145. tooluniverse/tools/dbsnp_search_by_gene.py +52 -0
  146. tooluniverse/tools/download_binary_file.py +66 -0
  147. tooluniverse/tools/download_file.py +71 -0
  148. tooluniverse/tools/download_text_content.py +55 -0
  149. tooluniverse/tools/dynamic_package_discovery.py +59 -0
  150. tooluniverse/tools/ensembl_get_sequence.py +52 -0
  151. tooluniverse/tools/{Ensembl_lookup_gene_by_symbol.py → ensembl_get_variants.py} +11 -11
  152. tooluniverse/tools/ensembl_lookup_gene.py +46 -0
  153. tooluniverse/tools/geo_get_dataset_info.py +46 -0
  154. tooluniverse/tools/geo_get_sample_info.py +46 -0
  155. tooluniverse/tools/geo_search_datasets.py +67 -0
  156. tooluniverse/tools/gnomad_get_gene_constraints.py +49 -0
  157. tooluniverse/tools/kegg_find_genes.py +52 -0
  158. tooluniverse/tools/kegg_get_gene_info.py +46 -0
  159. tooluniverse/tools/kegg_get_pathway_info.py +46 -0
  160. tooluniverse/tools/kegg_list_organisms.py +44 -0
  161. tooluniverse/tools/kegg_search_pathway.py +46 -0
  162. tooluniverse/tools/ols_find_similar_terms.py +63 -0
  163. tooluniverse/tools/{get_hyperopt_info.py → ols_get_ontology_info.py} +13 -10
  164. tooluniverse/tools/ols_get_term_ancestors.py +67 -0
  165. tooluniverse/tools/ols_get_term_children.py +67 -0
  166. tooluniverse/tools/{TestCaseGenerator.py → ols_get_term_info.py} +12 -9
  167. tooluniverse/tools/{CodeOptimizer.py → ols_search_ontologies.py} +22 -14
  168. tooluniverse/tools/ols_search_terms.py +71 -0
  169. tooluniverse/tools/python_code_executor.py +79 -0
  170. tooluniverse/tools/python_script_runner.py +79 -0
  171. tooluniverse/tools/web_api_documentation_search.py +63 -0
  172. tooluniverse/tools/web_search.py +71 -0
  173. tooluniverse/uniprot_tool.py +219 -16
  174. tooluniverse/url_tool.py +19 -1
  175. tooluniverse/uspto_tool.py +1 -1
  176. tooluniverse/utils.py +12 -12
  177. tooluniverse/web_search_tool.py +229 -0
  178. tooluniverse/worms_tool.py +64 -0
  179. {tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/METADATA +8 -3
  180. {tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/RECORD +184 -92
  181. tooluniverse/data/genomics_tools.json +0 -174
  182. tooluniverse/tools/ToolDescriptionOptimizer.py +0 -67
  183. tooluniverse/tools/ToolImplementationGenerator.py +0 -67
  184. tooluniverse/tools/ToolOptimizer.py +0 -59
  185. tooluniverse/tools/ToolSpecificationGenerator.py +0 -67
  186. tooluniverse/tools/ToolSpecificationOptimizer.py +0 -63
  187. tooluniverse/ucsc_tool.py +0 -60
  188. {tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/WHEEL +0 -0
  189. {tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/entry_points.txt +0 -0
  190. {tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/licenses/LICENSE +0 -0
  191. {tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/top_level.txt +0 -0
tooluniverse/compose_scripts/output_summarizer.py CHANGED
@@ -39,7 +39,7 @@ def compose(arguments: Dict[str, Any], tooluniverse, call_tool) -> Dict[str, Any
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  tooluniverse: ToolUniverse instance for tool execution
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  call_tool: Function to call other tools within the composition
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- Returns:
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+ Returns
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  Dict[str, Any]: Dictionary containing:
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  - success (bool): Whether summarization was successful
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  - original_length (int): Length of original output
@@ -165,7 +165,7 @@ def _chunk_output(text: str, chunk_size: int) -> List[str]:
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  text (str): The text to be chunked
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  chunk_size (int): Maximum size of each chunk
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- Returns:
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+ Returns
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  List[str]: List of text chunks
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  """
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  if len(text) <= chunk_size:
@@ -208,7 +208,7 @@ def _summarize_chunk(
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  focus_areas (str): Areas to focus on during summarization
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  call_tool: Function to call the summarizer tool
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- Returns:
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+ Returns
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  str: Summarized chunk text, or empty string if summarization fails
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  """
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  try:
@@ -296,7 +296,7 @@ def _merge_summaries(
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  max_length (int): Maximum length of final summary
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  call_tool: Function to call the summarizer tool
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- Returns:
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+ Returns
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  str: Final merged summary
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  """
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  if not chunk_summaries: