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

tooluniverse/data/uniprot_tools.json

@@ -207,5 +207,82 @@
         "output_description": "Returns a list containing all isoform ID strings."
       },
       "type": "UniProtRESTTool"
+    },
+    {
+      "name": "UniProt_search",
+      "description": "Search UniProtKB database using flexible query syntax. Supports gene names (e.g., 'gene:TP53'), protein names, organism filters (e.g., 'organism:9606'), and complex queries using AND/OR operators. Returns matching proteins with accession numbers and key information. Use this to find UniProt accessions from gene or protein names.",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "query": {
+            "type": "string",
+            "description": "Search query. Can be simple (e.g., 'MEIOB') or advanced ('gene:TP53 AND organism:9606'). Keywords: gene, protein_name, organism, reviewed, etc."
+          },
+          "organism": {
+            "type": "string",
+            "description": "Optional organism filter. Can use common name ('human') or taxonomy ID ('9606'). Automatically combined with query using AND."
+          },
+          "limit": {
+            "type": "integer",
+            "description": "Maximum number of results to return (default: 25, max: 500)"
+          },
+          "fields": {
+            "type": "array",
+            "items": {
+              "type": "string"
+            },
+            "description": "Optional list of fields to return. Default returns: accession, id, protein_name, gene_names, organism, length"
+          }
+        },
+        "required": ["query"]
+      },
+      "fields": {
+        "endpoint": "https://rest.uniprot.org/uniprotkb/search",
+        "search_type": "search",
+        "format": "json"
+      },
+      "type": "UniProtRESTTool"
+    },
+    {
+      "name": "UniProt_id_mapping",
+      "description": "Map IDs between different databases (e.g., Ensembl to UniProt, Gene Name to UniProt). Supports batch mapping and async task processing. Use this to convert between different database identifiers.",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "ids": {
+            "oneOf": [
+              {
+                "type": "array",
+                "items": {
+                  "type": "string"
+                }
+              },
+              {
+                "type": "string"
+              }
+            ],
+            "description": "ID(s) to map. Can be single string or array of strings, e.g., 'ENSG00000141510' or ['MEIOB', 'TP53']"
+          },
+          "from_db": {
+            "type": "string",
+            "description": "Source database. Examples: 'Ensembl', 'Gene_Name', 'RefSeq_Protein', 'PDB', 'EMBL'"
+          },
+          "to_db": {
+            "type": "string",
+            "description": "Target database (default: 'UniProtKB')"
+          },
+          "max_wait_time": {
+            "type": "integer",
+            "description": "Maximum time to wait for async task completion in seconds (default: 30)"
+          }
+        },
+        "required": ["ids", "from_db"]
+      },
+      "fields": {
+        "endpoint": "https://rest.uniprot.org/idmapping",
+        "mapping_type": "async",
+        "format": "json"
+      },
+      "type": "UniProtRESTTool"
     }
   ]

tooluniverse/data/web_search_tools.json

@@ -0,0 +1,250 @@
+[
+  {
+    "type": "WebSearchTool",
+    "name": "web_search",
+    "description": "General web search using DDGS (Dux Distributed Global Search) supporting multiple search engines including Google, Bing, Brave, Yahoo, and DuckDuckGo. No API keys required.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "Search query string"
+        },
+        "max_results": {
+          "type": "integer",
+          "description": "Maximum number of results to return",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 50
+        },
+        "search_type": {
+          "type": "string",
+          "description": "Type of search to perform",
+          "enum": ["general", "api_documentation", "python_packages", "github"],
+          "default": "general"
+        },
+        "backend": {
+          "type": "string",
+          "description": "Search engine backend to use",
+          "enum": ["auto", "google", "bing", "brave", "yahoo", "duckduckgo"],
+          "default": "auto"
+        },
+        "region": {
+          "type": "string",
+          "description": "Search region/locale",
+          "enum": ["us-en", "cn-zh", "uk-en", "de-de", "fr-fr", "ja-jp"],
+          "default": "us-en"
+        },
+        "safesearch": {
+          "type": "string",
+          "description": "Safe search level",
+          "enum": ["on", "moderate", "off"],
+          "default": "moderate"
+        }
+      },
+      "required": ["query"]
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the search operation",
+          "enum": ["success", "error"]
+        },
+        "query": {
+          "type": "string",
+          "description": "The search query that was executed"
+        },
+        "search_type": {
+          "type": "string",
+          "description": "Type of search that was performed"
+        },
+        "total_results": {
+          "type": "integer",
+          "description": "Total number of results found"
+        },
+        "results": {
+          "type": "array",
+          "description": "Array of search results",
+          "items": {
+            "type": "object",
+            "properties": {
+              "title": {
+                "type": "string",
+                "description": "Title of the search result"
+              },
+              "url": {
+                "type": "string",
+                "description": "URL of the search result"
+              },
+              "snippet": {
+                "type": "string",
+                "description": "Snippet or description of the result"
+              },
+              "rank": {
+                "type": "integer",
+                "description": "Rank of the result in search results"
+              }
+            },
+            "required": ["title", "url", "snippet", "rank"]
+          }
+        },
+        "error": {
+          "type": "string",
+          "description": "Error message if status is error"
+        }
+      },
+      "required": ["status", "query", "total_results", "results"]
+    },
+    "test_examples": [
+      {
+        "input": {
+          "query": "python requests library",
+          "max_results": 5
+        },
+        "expected_output_type": "object",
+        "description": "Search for Python requests library information"
+      },
+      {
+        "input": {
+          "query": "machine learning APIs",
+          "search_type": "api_documentation",
+          "max_results": 3
+        },
+        "expected_output_type": "object",
+        "description": "Search for machine learning API documentation"
+      }
+    ],
+    "metadata": {
+      "tags": ["web-search", "multi-engine", "no-api-key", "ddgs"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "2-5 seconds"
+    }
+  },
+  {
+    "type": "WebAPIDocumentationSearchTool",
+    "name": "web_api_documentation_search",
+    "description": "Specialized web search for API documentation, Python packages, and technical resources using DDGS with multiple search engines. Optimized for finding official documentation and library information.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "Search query string (e.g., tool name, library name, API name)"
+        },
+        "max_results": {
+          "type": "integer",
+          "description": "Maximum number of results to return",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 50
+        },
+        "focus": {
+          "type": "string",
+          "description": "Focus area for the search",
+          "enum": ["api_docs", "python_packages", "github_repos"],
+          "default": "api_docs"
+        },
+        "backend": {
+          "type": "string",
+          "description": "Search engine backend to use",
+          "enum": ["auto", "google", "bing", "brave", "yahoo", "duckduckgo"],
+          "default": "auto"
+        }
+      },
+      "required": ["query"]
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the search operation",
+          "enum": ["success", "error"]
+        },
+        "query": {
+          "type": "string",
+          "description": "The search query that was executed"
+        },
+        "focus": {
+          "type": "string",
+          "description": "Focus area that was used for the search"
+        },
+        "enhanced_query": {
+          "type": "string",
+          "description": "Enhanced query that was actually executed"
+        },
+        "total_results": {
+          "type": "integer",
+          "description": "Total number of results found"
+        },
+        "results": {
+          "type": "array",
+          "description": "Array of search results",
+          "items": {
+            "type": "object",
+            "properties": {
+              "title": {
+                "type": "string",
+                "description": "Title of the search result"
+              },
+              "url": {
+                "type": "string",
+                "description": "URL of the search result"
+              },
+              "snippet": {
+                "type": "string",
+                "description": "Snippet or description of the result"
+              },
+              "rank": {
+                "type": "integer",
+                "description": "Rank of the result in search results"
+              }
+            },
+            "required": ["title", "url", "snippet", "rank"]
+          }
+        },
+        "error": {
+          "type": "string",
+          "description": "Error message if status is error"
+        }
+      },
+      "required": ["status", "query", "total_results", "results"]
+    },
+    "test_examples": [
+      {
+        "input": {
+          "query": "pandas",
+          "focus": "api_docs",
+          "max_results": 5
+        },
+        "expected_output_type": "object",
+        "description": "Search for pandas API documentation"
+      },
+      {
+        "input": {
+          "query": "requests",
+          "focus": "python_packages",
+          "max_results": 3
+        },
+        "expected_output_type": "object",
+        "description": "Search for requests Python package information"
+      },
+      {
+        "input": {
+          "query": "scikit-learn",
+          "focus": "github_repos",
+          "max_results": 3
+        },
+        "expected_output_type": "object",
+        "description": "Search for scikit-learn GitHub repositories"
+      }
+    ],
+    "metadata": {
+      "tags": ["web-search", "api-documentation", "python-packages", "technical-resources", "multi-engine", "ddgs"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "2-5 seconds"
+    }
+  }
+]

tooluniverse/data/worms_tools.json

@@ -0,0 +1,55 @@
+[
+  {
+    "type": "WoRMSRESTTool",
+    "name": "WoRMS_search_species",
+    "description": "Search marine species in World Register of Marine Species",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {"type": "string", "description": "Species name or search term"},
+        "limit": {"type": "integer", "default": 20, "description": "Number of results"}
+      },
+      "required": ["query"]
+    },
+    "fields": {
+      "endpoint": "https://www.marinespecies.org/rest/AphiaIDByName/{query}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "AphiaID": {"type": "integer"},
+        "url": {"type": "string"},
+        "scientificname": {"type": "string"},
+        "authority": {"type": "string"},
+        "status": {"type": "string"},
+        "unacceptreason": {"type": "string"},
+        "taxonRankID": {"type": "integer"},
+        "rank": {"type": "string"},
+        "valid_AphiaID": {"type": "integer"},
+        "valid_name": {"type": "string"},
+        "valid_authority": {"type": "string"},
+        "parentNameUsageID": {"type": "integer"},
+        "kingdom": {"type": "string"},
+        "phylum": {"type": "string"},
+        "class": {"type": "string"},
+        "order": {"type": "string"},
+        "family": {"type": "string"},
+        "genus": {"type": "string"},
+        "citation": {"type": "string"},
+        "lsid": {"type": "string"},
+        "isMarine": {"type": "boolean"},
+        "isBrackish": {"type": "boolean"},
+        "isFreshwater": {"type": "boolean"},
+        "isTerrestrial": {"type": "boolean"},
+        "isExtinct": {"type": "boolean"},
+        "match_type": {"type": "string"},
+        "modified": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"query": "Actinia equina", "limit": 5},
+      {"query": "Scleractinia", "limit": 10}
+    ]
+  }
+]

tooluniverse/dataset_tool.py

@@ -123,7 +123,7 @@ class DatasetTool(BaseTool):
                 - exact_match (bool): Whether to perform exact matching
                 - limit (int): Maximum number of results
 
-        Returns:
+        Returns
             dict: Search results with matched records and metadata
         """
         query = arguments.get("query", "")
@@ -206,7 +206,7 @@ class DatasetTool(BaseTool):
                 - value (str): Value to filter by (optional for not_empty condition)
                 - limit (int): Maximum number of results
 
-        Returns:
+        Returns
             dict: Filtered results with matched records and applied filters
         """
         field = arguments.get("field")