PyPI - tooluniverse - Versions diffs - 1.0.9.1__py3-none-any.whl → 1.0.11__py3-none-any.whl - Mend

tooluniverse 1.0.9.1py3-none-any.whl → 1.0.11py3-none-any.whl

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tooluniverse/__init__.py +57 -1
tooluniverse/admetai_tool.py +1 -1
tooluniverse/agentic_tool.py +65 -17
tooluniverse/base_tool.py +19 -8
tooluniverse/blast_tool.py +132 -0
tooluniverse/boltz_tool.py +3 -3
tooluniverse/cache/result_cache_manager.py +167 -12
tooluniverse/cbioportal_tool.py +42 -0
tooluniverse/clinvar_tool.py +268 -74
tooluniverse/compose_scripts/drug_safety_analyzer.py +1 -1
tooluniverse/compose_scripts/multi_agent_literature_search.py +1 -1
tooluniverse/compose_scripts/output_summarizer.py +4 -4
tooluniverse/compose_scripts/tool_discover.py +1941 -443
tooluniverse/compose_scripts/tool_graph_composer.py +1 -1
tooluniverse/compose_scripts/tool_metadata_generator.py +1 -1
tooluniverse/compose_tool.py +9 -9
tooluniverse/core_tool.py +2 -2
tooluniverse/ctg_tool.py +4 -4
tooluniverse/custom_tool.py +1 -1
tooluniverse/data/agentic_tools.json +0 -370
tooluniverse/data/alphafold_tools.json +6 -6
tooluniverse/data/blast_tools.json +112 -0
tooluniverse/data/cbioportal_tools.json +87 -0
tooluniverse/data/clinvar_tools.json +235 -0
tooluniverse/data/compose_tools.json +0 -89
tooluniverse/data/dbsnp_tools.json +275 -0
tooluniverse/data/emdb_tools.json +61 -0
tooluniverse/data/ensembl_tools.json +259 -0
tooluniverse/data/file_download_tools.json +275 -0
tooluniverse/data/geo_tools.json +200 -48
tooluniverse/data/gnomad_tools.json +109 -0
tooluniverse/data/gtopdb_tools.json +68 -0
tooluniverse/data/gwas_tools.json +32 -0
tooluniverse/data/interpro_tools.json +199 -0
tooluniverse/data/jaspar_tools.json +70 -0
tooluniverse/data/kegg_tools.json +356 -0
tooluniverse/data/mpd_tools.json +87 -0
tooluniverse/data/ols_tools.json +314 -0
tooluniverse/data/package_discovery_tools.json +64 -0
tooluniverse/data/packages/categorized_tools.txt +0 -1
tooluniverse/data/packages/machine_learning_tools.json +0 -47
tooluniverse/data/paleobiology_tools.json +91 -0
tooluniverse/data/pride_tools.json +62 -0
tooluniverse/data/pypi_package_inspector_tools.json +158 -0
tooluniverse/data/python_executor_tools.json +341 -0
tooluniverse/data/regulomedb_tools.json +50 -0
tooluniverse/data/remap_tools.json +89 -0
tooluniverse/data/screen_tools.json +89 -0
tooluniverse/data/tool_discovery_agents.json +428 -0
tooluniverse/data/tool_discovery_agents.json.backup +1343 -0
tooluniverse/data/uniprot_tools.json +77 -0
tooluniverse/data/web_search_tools.json +250 -0
tooluniverse/data/worms_tools.json +55 -0
tooluniverse/dataset_tool.py +2 -2
tooluniverse/dbsnp_tool.py +196 -58
tooluniverse/default_config.py +36 -3
tooluniverse/emdb_tool.py +30 -0
tooluniverse/enrichr_tool.py +14 -14
tooluniverse/ensembl_tool.py +140 -47
tooluniverse/execute_function.py +594 -29
tooluniverse/extended_hooks.py +4 -4
tooluniverse/file_download_tool.py +269 -0
tooluniverse/gene_ontology_tool.py +1 -1
tooluniverse/generate_tools.py +3 -3
tooluniverse/geo_tool.py +81 -28
tooluniverse/gnomad_tool.py +100 -52
tooluniverse/gtopdb_tool.py +41 -0
tooluniverse/humanbase_tool.py +10 -10
tooluniverse/interpro_tool.py +72 -0
tooluniverse/jaspar_tool.py +30 -0
tooluniverse/kegg_tool.py +230 -0
tooluniverse/logging_config.py +2 -2
tooluniverse/mcp_client_tool.py +57 -129
tooluniverse/mcp_integration.py +52 -49
tooluniverse/mcp_tool_registry.py +147 -528
tooluniverse/mpd_tool.py +42 -0
tooluniverse/ncbi_eutils_tool.py +96 -0
tooluniverse/ols_tool.py +435 -0
tooluniverse/openalex_tool.py +8 -8
tooluniverse/openfda_tool.py +2 -2
tooluniverse/output_hook.py +15 -15
tooluniverse/package_discovery_tool.py +217 -0
tooluniverse/package_tool.py +1 -1
tooluniverse/paleobiology_tool.py +30 -0
tooluniverse/pmc_tool.py +2 -2
tooluniverse/pride_tool.py +30 -0
tooluniverse/pypi_package_inspector_tool.py +593 -0
tooluniverse/python_executor_tool.py +711 -0
tooluniverse/regulomedb_tool.py +30 -0
tooluniverse/remap_tool.py +44 -0
tooluniverse/remote/boltz/boltz_mcp_server.py +1 -1
tooluniverse/remote/depmap_24q2/depmap_24q2_mcp_tool.py +3 -3
tooluniverse/remote/immune_compass/compass_tool.py +3 -3
tooluniverse/remote/pinnacle/pinnacle_tool.py +2 -2
tooluniverse/remote/transcriptformer/transcriptformer_tool.py +3 -3
tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +3 -3
tooluniverse/remote_tool.py +4 -4
tooluniverse/screen_tool.py +44 -0
tooluniverse/scripts/filter_tool_files.py +2 -2
tooluniverse/smcp.py +93 -12
tooluniverse/smcp_server.py +100 -21
tooluniverse/space/__init__.py +46 -0
tooluniverse/space/loader.py +133 -0
tooluniverse/space/validator.py +353 -0
tooluniverse/tool_finder_embedding.py +5 -3
tooluniverse/tool_finder_keyword.py +12 -10
tooluniverse/tool_finder_llm.py +12 -8
tooluniverse/tools/{UCSC_get_genes_by_region.py → BLAST_nucleotide_search.py} +22 -26
tooluniverse/tools/BLAST_protein_search.py +63 -0
tooluniverse/tools/ClinVar_search_variants.py +26 -15
tooluniverse/tools/CodeQualityAnalyzer.py +3 -3
tooluniverse/tools/EMDB_get_structure.py +46 -0
tooluniverse/tools/GtoPdb_get_targets.py +52 -0
tooluniverse/tools/InterPro_get_domain_details.py +46 -0
tooluniverse/tools/InterPro_get_protein_domains.py +49 -0
tooluniverse/tools/InterPro_search_domains.py +52 -0
tooluniverse/tools/JASPAR_get_transcription_factors.py +52 -0
tooluniverse/tools/MPD_get_phenotype_data.py +59 -0
tooluniverse/tools/PRIDE_search_proteomics.py +52 -0
tooluniverse/tools/PackageAnalyzer.py +55 -0
tooluniverse/tools/Paleobiology_get_fossils.py +52 -0
tooluniverse/tools/PyPIPackageInspector.py +59 -0
tooluniverse/tools/ReMap_get_transcription_factor_binding.py +59 -0
tooluniverse/tools/ReferenceInfoAnalyzer.py +55 -0
tooluniverse/tools/RegulomeDB_query_variant.py +46 -0
tooluniverse/tools/SCREEN_get_regulatory_elements.py +59 -0
tooluniverse/tools/{ArgumentDescriptionOptimizer.py → TestResultsAnalyzer.py} +13 -13
tooluniverse/tools/ToolDiscover.py +11 -11
tooluniverse/tools/UniProt_id_mapping.py +63 -0
tooluniverse/tools/UniProt_search.py +63 -0
tooluniverse/tools/UnifiedToolGenerator.py +59 -0
tooluniverse/tools/WoRMS_search_species.py +49 -0
tooluniverse/tools/XMLToolOptimizer.py +55 -0
tooluniverse/tools/__init__.py +119 -29
tooluniverse/tools/_shared_client.py +3 -3
tooluniverse/tools/alphafold_get_annotations.py +3 -3
tooluniverse/tools/alphafold_get_prediction.py +3 -3
tooluniverse/tools/alphafold_get_summary.py +3 -3
tooluniverse/tools/cBioPortal_get_cancer_studies.py +46 -0
tooluniverse/tools/cBioPortal_get_mutations.py +52 -0
tooluniverse/tools/{gnomAD_query_variant.py → clinvar_get_clinical_significance.py} +8 -11
tooluniverse/tools/clinvar_get_variant_details.py +49 -0
tooluniverse/tools/dbSNP_get_variant_by_rsid.py +7 -7
tooluniverse/tools/dbsnp_get_frequencies.py +46 -0
tooluniverse/tools/dbsnp_search_by_gene.py +52 -0
tooluniverse/tools/download_binary_file.py +66 -0
tooluniverse/tools/download_file.py +71 -0
tooluniverse/tools/download_text_content.py +55 -0
tooluniverse/tools/dynamic_package_discovery.py +59 -0
tooluniverse/tools/ensembl_get_sequence.py +52 -0
tooluniverse/tools/{Ensembl_lookup_gene_by_symbol.py → ensembl_get_variants.py} +11 -11
tooluniverse/tools/ensembl_lookup_gene.py +46 -0
tooluniverse/tools/geo_get_dataset_info.py +46 -0
tooluniverse/tools/geo_get_sample_info.py +46 -0
tooluniverse/tools/geo_search_datasets.py +67 -0
tooluniverse/tools/gnomad_get_gene_constraints.py +49 -0
tooluniverse/tools/kegg_find_genes.py +52 -0
tooluniverse/tools/kegg_get_gene_info.py +46 -0
tooluniverse/tools/kegg_get_pathway_info.py +46 -0
tooluniverse/tools/kegg_list_organisms.py +44 -0
tooluniverse/tools/kegg_search_pathway.py +46 -0
tooluniverse/tools/ols_find_similar_terms.py +63 -0
tooluniverse/tools/{get_hyperopt_info.py → ols_get_ontology_info.py} +13 -10
tooluniverse/tools/ols_get_term_ancestors.py +67 -0
tooluniverse/tools/ols_get_term_children.py +67 -0
tooluniverse/tools/{TestCaseGenerator.py → ols_get_term_info.py} +12 -9
tooluniverse/tools/{CodeOptimizer.py → ols_search_ontologies.py} +22 -14
tooluniverse/tools/ols_search_terms.py +71 -0
tooluniverse/tools/python_code_executor.py +79 -0
tooluniverse/tools/python_script_runner.py +79 -0
tooluniverse/tools/web_api_documentation_search.py +63 -0
tooluniverse/tools/web_search.py +71 -0
tooluniverse/uniprot_tool.py +219 -16
tooluniverse/url_tool.py +19 -1
tooluniverse/uspto_tool.py +1 -1
tooluniverse/utils.py +12 -12
tooluniverse/web_search_tool.py +229 -0
tooluniverse/worms_tool.py +64 -0
{tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/METADATA +8 -3
{tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/RECORD +184 -92
tooluniverse/data/genomics_tools.json +0 -174
tooluniverse/tools/ToolDescriptionOptimizer.py +0 -67
tooluniverse/tools/ToolImplementationGenerator.py +0 -67
tooluniverse/tools/ToolOptimizer.py +0 -59
tooluniverse/tools/ToolSpecificationGenerator.py +0 -67
tooluniverse/tools/ToolSpecificationOptimizer.py +0 -63
tooluniverse/ucsc_tool.py +0 -60
{tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/WHEEL +0 -0
{tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/entry_points.txt +0 -0
{tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/licenses/LICENSE +0 -0
{tooluniverse-1.0.9.1.dist-info → tooluniverse-1.0.11.dist-info}/top_level.txt +0 -0

tooluniverse/data/gtopdb_tools.json ADDED Viewed

@@ -0,0 +1,68 @@
+[
+  {
+    "type": "GtoPdbRESTTool",
+    "name": "GtoPdb_get_targets",
+    "description": "Get pharmacological targets from Guide to Pharmacology database",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "target_type": {"type": "string", "default": "protein", "description": "Target type"},
+        "limit": {"type": "integer", "default": 20, "description": "Number of results"}
+      }
+    },
+    "fields": {
+      "endpoint": "https://www.guidetopharmacology.org/services/targets",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "targetId": {"type": "integer"},
+          "name": {"type": "string"},
+          "targetType": {"type": "string"},
+          "species": {"type": "string"},
+          "uniprotId": {"type": "string"},
+          "ensemblGeneId": {"type": "string"},
+          "hgncId": {"type": "string"},
+          "description": {"type": "string"},
+          "family": {"type": "string"},
+          "subfamily": {"type": "string"},
+          "subunit": {"type": "string"},
+          "tissue": {"type": "array"},
+          "cellLine": {"type": "array"},
+          "diseases": {"type": "array"},
+          "drugs": {
+            "type": "array",
+            "items": {
+              "type": "object",
+              "properties": {
+                "drugId": {"type": "integer"},
+                "name": {"type": "string"},
+                "action": {"type": "string"},
+                "mechanism": {"type": "string"}
+              }
+            }
+          },
+          "ligands": {
+            "type": "array",
+            "items": {
+              "type": "object",
+              "properties": {
+                "ligandId": {"type": "integer"},
+                "name": {"type": "string"},
+                "type": {"type": "string"},
+                "affinity": {"type": "string"}
+              }
+            }
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {"target_type": "protein", "limit": 5},
+      {"target_type": "receptor", "limit": 10}
+    ]
+  }
+]

tooluniverse/data/gwas_tools.json CHANGED Viewed

@@ -1839,5 +1839,37 @@
         }
       }
     }
+  },
+  {
+    "type": "GWASGeneSearch",
+    "name": "GWAS_search_associations_by_gene",
+    "description": "Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene_name": {"type": "string", "description": "Gene symbol (e.g., BRCA1)."},
+        "size": {"type": "integer", "description": "Max associations to return.", "default": 5}
+      },
+      "required": ["gene_name"]
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "gene_name": {"type": "string"},
+        "association_count": {"type": "integer"},
+        "associations": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "study": {"type": "string"},
+              "strongestRiskAllele": {"type": "string"},
+              "pvalue": {"type": "number"}
+            }
+          }
+        },
+        "total_found": {"type": "integer"}
+      }
+    }
   }
 ]

tooluniverse/data/interpro_tools.json ADDED Viewed

@@ -0,0 +1,199 @@
+[
+  {
+    "type": "InterProRESTTool",
+    "name": "InterPro_get_protein_domains",
+    "description": "Get protein domain annotations from InterPro database using UniProt protein ID. Returns domain families, signatures, and functional annotations.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "protein_id": {
+          "type": "string",
+          "description": "UniProt protein ID (e.g., P05067, Q9Y6K9)"
+        }
+      },
+      "required": ["protein_id"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/UniProt/{protein_id}",
+      "extract_path": "results",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "array",
+      "description": "List of InterPro entries for the protein",
+      "items": {
+        "type": "object",
+        "properties": {
+          "metadata": {
+            "type": "object",
+            "properties": {
+              "accession": {"type": "string"},
+              "name": {"type": "string"},
+              "type": {"type": "string"},
+              "source_database": {"type": "string"},
+              "integrated": {"type": "string"},
+              "member_databases": {"type": "object"},
+              "go_terms": {
+                "type": "array",
+                "items": {
+                  "type": "object",
+                  "properties": {
+                    "identifier": {"type": "string"},
+                    "name": {"type": "string"},
+                    "category": {
+                      "type": "object",
+                      "properties": {
+                        "code": {"type": "string"},
+                        "name": {"type": "string"}
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          },
+          "proteins": {
+            "type": "array",
+            "items": {
+              "type": "object",
+              "properties": {
+                "accession": {"type": "string"},
+                "protein_length": {"type": "integer"},
+                "source_database": {"type": "string"},
+                "organism": {"type": "string"},
+                "in_alphafold": {"type": "boolean"},
+                "in_bfvd": {"type": "boolean"},
+                "entry_protein_locations": {
+                  "type": "array",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "fragments": {"type": "array"},
+                      "representative": {"type": "boolean"},
+                      "model": {"type": "string"},
+                      "score": {"type": "number"}
+                    }
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "protein_id": "P05067"
+      },
+      {
+        "protein_id": "Q9Y6K9"
+      }
+    ]
+  },
+  {
+    "type": "InterProRESTTool",
+    "name": "InterPro_search_domains",
+    "description": "Search InterPro database for protein domains and families by name or accession. Returns matching domain entries with metadata.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "Domain name, accession, or search term (e.g., 'kinase', 'IPR000719')"
+        },
+        "size": {
+          "type": "integer",
+          "description": "Number of results to return (default: 20, max: 100)",
+          "default": 20,
+          "minimum": 1,
+          "maximum": 100
+        }
+      },
+      "required": ["query"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/interpro/api/entry/interpro/search?query={query}&size={size}",
+      "extract_path": "results",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "array",
+      "description": "List of matching InterPro entries",
+      "items": {
+        "type": "object",
+        "properties": {
+          "metadata": {
+            "type": "object",
+            "properties": {
+              "accession": {"type": "string"},
+              "name": {"type": "string"},
+              "type": {"type": "string"},
+              "source_database": {"type": "string"}
+            }
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "query": "kinase",
+        "size": 5
+      },
+      {
+        "query": "IPR000719",
+        "size": 1
+      }
+    ]
+  },
+  {
+    "type": "InterProRESTTool",
+    "name": "InterPro_get_domain_details",
+    "description": "Get detailed information about a specific InterPro domain entry including description, hierarchy, and member databases.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "accession": {
+          "type": "string",
+          "description": "InterPro accession ID (e.g., IPR000719, IPR000719)"
+        }
+      },
+      "required": ["accession"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/interpro/api/entry/interpro/{accession}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Detailed InterPro entry information",
+      "properties": {
+        "metadata": {
+          "type": "object",
+          "properties": {
+            "accession": {"type": "string"},
+            "name": {"type": "string"},
+            "type": {"type": "string"},
+            "source_database": {"type": "string"},
+            "description": {"type": "string"}
+          }
+        },
+        "hierarchy": {
+          "type": "object",
+          "description": "Domain hierarchy information"
+        },
+        "member_databases": {
+          "type": "object",
+          "description": "Member database signatures"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "accession": "IPR000719"
+      },
+      {
+        "accession": "IPR000719"
+      }
+    ]
+  }
+]

tooluniverse/data/jaspar_tools.json ADDED Viewed

@@ -0,0 +1,70 @@
+[
+  {
+    "type": "JASPARRESTTool",
+    "name": "JASPAR_get_transcription_factors",
+    "description": "Get transcription factor binding site matrices from JASPAR",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "collection": {"type": "string", "default": "CORE", "description": "JASPAR collection"},
+        "limit": {"type": "integer", "default": 20, "description": "Number of results"}
+      }
+    },
+    "fields": {
+      "endpoint": "https://jaspar.elixir.no/api/v1/matrix/?collection={collection}&limit={limit}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "results": {
+          "type": "array",
+          "items": {
+            "type": "object",
+            "properties": {
+              "matrix_id": {"type": "string"},
+              "name": {"type": "string"},
+              "collection": {"type": "string"},
+              "species": {"type": "array"},
+              "class": {"type": "string"},
+              "family": {"type": "string"},
+              "tax_group": {"type": "string"},
+              "type": {"type": "string"},
+              "version": {"type": "integer"},
+              "base_id": {"type": "string"},
+              "uniprot_ids": {"type": "array"},
+              "data_type": {"type": "string"},
+              "pubmed_id": {"type": "array"},
+              "jaspar_id": {"type": "string"},
+              "pfm": {
+                "type": "object",
+                "properties": {
+                  "A": {"type": "array"},
+                  "C": {"type": "array"},
+                  "G": {"type": "array"},
+                  "T": {"type": "array"}
+                }
+              },
+              "pwm": {
+                "type": "object",
+                "properties": {
+                  "A": {"type": "array"},
+                  "C": {"type": "array"},
+                  "G": {"type": "array"},
+                  "T": {"type": "array"}
+                }
+              }
+            }
+          }
+        },
+        "count": {"type": "integer"},
+        "next": {"type": "string"},
+        "previous": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"collection": "CORE", "limit": 5},
+      {"collection": "CNE", "limit": 10}
+    ]
+  }
+]

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

Potentially problematic release.

tooluniverse 1.0.9.1py3-none-any.whl → 1.0.11py3-none-any.whl