tooluniverse 1.0.10__py3-none-any.whl → 1.0.11.1__py3-none-any.whl

tooluniverse/data/emdb_tools.json

@@ -0,0 +1,61 @@
+[
+  {
+    "type": "EMDBRESTTool",
+    "name": "EMDB_get_structure",
+    "description": "Get electron microscopy structure data from EMDB",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "emdb_id": {"type": "string", "description": "EMDB structure ID (e.g., EMD-1234)"}
+      },
+      "required": ["emdb_id"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/emdb/api/entry/{emdb_id}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "emdb_id": {"type": "string"},
+        "title": {"type": "string"},
+        "description": {"type": "string"},
+        "resolution": {"type": "number"},
+        "method": {"type": "string"},
+        "organism": {"type": "string"},
+        "molecule": {"type": "string"},
+        "deposition_date": {"type": "string"},
+        "release_date": {"type": "string"},
+        "authors": {"type": "array"},
+        "journal": {"type": "string"},
+        "volume": {"type": "string"},
+        "page": {"type": "string"},
+        "year": {"type": "integer"},
+        "doi": {"type": "string"},
+        "pdb_id": {"type": "string"},
+        "map_url": {"type": "string"},
+        "contour_level": {"type": "number"},
+        "voxel_size": {
+          "type": "object",
+          "properties": {
+            "x": {"type": "number"},
+            "y": {"type": "number"},
+            "z": {"type": "number"}
+          }
+        },
+        "map_dimensions": {
+          "type": "object",
+          "properties": {
+            "x": {"type": "integer"},
+            "y": {"type": "integer"},
+            "z": {"type": "integer"}
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {"emdb_id": "EMD-1234"},
+      {"emdb_id": "EMD-0001"}
+    ]
+  }
+]

tooluniverse/data/ensembl_tools.json

@@ -0,0 +1,259 @@
+[
+  {
+    "type": "EnsemblLookupGene",
+    "name": "ensembl_lookup_gene",
+    "description": "Lookup gene information by Ensembl gene ID or symbol. Returns gene details including location, description, and external references.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene_id": {
+          "type": "string",
+          "description": "Ensembl gene ID or symbol (e.g., 'ENSG00000139618' or 'BRCA1')"
+        }
+      },
+      "required": ["gene_id"]
+    },
+    "fields": {
+      "endpoint": "/lookup/id",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Ensembl gene lookup data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Gene information object",
+          "properties": {
+            "id": {
+              "type": "string",
+              "description": "Ensembl gene ID"
+            },
+            "display_name": {
+              "type": "string",
+              "description": "Gene symbol"
+            },
+            "description": {
+              "type": "string",
+              "description": "Gene description"
+            },
+            "biotype": {
+              "type": "string",
+              "description": "Gene biotype"
+            },
+            "start": {
+              "type": "integer",
+              "description": "Gene start position"
+            },
+            "end": {
+              "type": "integer",
+              "description": "Gene end position"
+            },
+            "strand": {
+              "type": "integer",
+              "description": "Gene strand"
+            },
+            "seq_region_name": {
+              "type": "string",
+              "description": "Chromosome name"
+            }
+          }
+        },
+        "gene_id": {
+          "type": "string",
+          "description": "Input gene ID"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "description": "Lookup BRCA1 gene information",
+        "input": {
+          "gene_id": "ENSG00000012048"
+        },
+        "expected_output": {
+          "status": "success",
+          "data": "Gene information object with BRCA1 details"
+        }
+      }
+    ],
+    "metadata": {
+      "tags": ["gene", "lookup", "annotation"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "type": "EnsemblGetSequence",
+    "name": "ensembl_get_sequence",
+    "description": "Get DNA sequence for a gene, transcript, or genomic region. Returns sequence in FASTA format.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "sequence_id": {
+          "type": "string",
+          "description": "Ensembl gene/transcript ID or genomic region (e.g., 'ENSG00000139618' or '1:1000000-2000000')"
+        },
+        "type": {
+          "type": "string",
+          "description": "Sequence type: 'genomic', 'cds', 'cdna', 'peptide'",
+          "default": "genomic"
+        }
+      },
+      "required": ["sequence_id"]
+    },
+    "fields": {
+      "endpoint": "/sequence/id",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Ensembl sequence data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "array",
+          "description": "Array of sequence objects",
+          "items": {
+            "type": "object",
+            "properties": {
+              "id": {
+                "type": "string",
+                "description": "Sequence ID"
+              },
+              "seq": {
+                "type": "string",
+                "description": "DNA/protein sequence"
+              },
+              "desc": {
+                "type": "string",
+                "description": "Sequence description"
+              },
+              "molecule": {
+                "type": "string",
+                "description": "Molecule type (dna, rna, protein)"
+              }
+            }
+          }
+        },
+        "sequence_id": {
+          "type": "string",
+          "description": "Input sequence ID"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "description": "Get genomic sequence for BRCA1 gene",
+        "input": {
+          "sequence_id": "ENSG00000012048",
+          "type": "genomic"
+        },
+        "expected_output": {
+          "status": "success",
+          "data": "Array with sequence object containing BRCA1 genomic sequence"
+        }
+      }
+    ],
+    "metadata": {
+      "tags": ["sequence", "dna", "genomic"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 3 seconds"
+    }
+  },
+  {
+    "type": "EnsemblGetVariants",
+    "name": "ensembl_get_variants",
+    "description": "Get genetic variants in a genomic region. Returns SNP and indel information.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "region": {
+          "type": "string",
+          "description": "Genomic region in format 'chromosome:start-end' (e.g., '13:32315086-32400268')"
+        },
+        "species": {
+          "type": "string",
+          "description": "Species name",
+          "default": "homo_sapiens"
+        }
+      },
+      "required": ["region"]
+    },
+    "fields": {
+      "endpoint": "/overlap/region",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "Ensembl variant data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "array",
+          "description": "Array of variant objects",
+          "items": {
+            "type": "object",
+            "properties": {
+              "id": {
+                "type": "string",
+                "description": "Variant ID"
+              },
+              "start": {
+                "type": "integer",
+                "description": "Variant start position"
+              },
+              "end": {
+                "type": "integer",
+                "description": "Variant end position"
+              },
+              "strand": {
+                "type": "integer",
+                "description": "Variant strand"
+              },
+              "allele_string": {
+                "type": "string",
+                "description": "Allele string (e.g., 'A/T')"
+              },
+              "consequence_type": {
+                "type": "string",
+                "description": "Variant consequence"
+              }
+            }
+          }
+        },
+        "region": {
+          "type": "string",
+          "description": "Input genomic region"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "description": "Get variants in BRCA1 region",
+        "input": {
+          "region": "13:32315086-32400268"
+        },
+        "expected_output": {
+          "status": "success",
+          "data": "Array of variant objects in BRCA1 region"
+        }
+      }
+    ],
+    "metadata": {
+      "tags": ["variants", "snp", "indel"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  }
+]

tooluniverse/data/file_download_tools.json

@@ -0,0 +1,275 @@
+[
+  {
+    "type": "FileDownloadTool",
+    "name": "download_file",
+    "description": "Download files from HTTP/HTTPS URLs with cross-platform support (Windows, Mac, Linux). Similar to curl but platform-independent. Can save to specified path or temporary directory.",
+    "fields": {
+      "return_key": "file_path"
+    },
+    "parameter": {
+      "type": "object",
+      "required": [
+        "url"
+      ],
+      "additionalProperties": false,
+      "properties": {
+        "url": {
+          "type": "string",
+          "description": "HTTP or HTTPS URL to download from (e.g., https://example.com/file.txt)",
+          "format": "uri"
+        },
+        "output_path": {
+          "type": "string",
+          "description": "Optional path to save the file. If not specified, file will be saved to system temp directory.",
+          "example": "/tmp/downloaded_file.txt or C:\\Users\\Downloads\\file.txt"
+        },
+        "timeout": {
+          "type": "integer",
+          "description": "Request timeout in seconds",
+          "minimum": 1,
+          "maximum": 300,
+          "default": 30
+        },
+        "return_content": {
+          "type": "boolean",
+          "description": "If true, return file content as text instead of saving to disk (default: false)",
+          "default": false
+        },
+        "chunk_size": {
+          "type": "integer",
+          "description": "Download chunk size in bytes (default: 8192)",
+          "minimum": 1024,
+          "maximum": 10485760,
+          "default": 8192
+        },
+        "follow_redirects": {
+          "type": "boolean",
+          "description": "Follow HTTP redirects (default: true)",
+          "default": true
+        }
+      }
+    },
+    "return_schema": {
+      "oneOf": [
+        {
+          "type": "object",
+          "description": "Successfully downloaded file",
+          "properties": {
+            "file_path": {
+              "type": "string",
+              "description": "Absolute path to the downloaded file"
+            },
+            "file_size": {
+              "type": "integer",
+              "description": "Size of the file in bytes"
+            },
+            "url": {
+              "type": "string",
+              "description": "Original URL that was downloaded"
+            },
+            "content_type": {
+              "type": "string",
+              "description": "MIME type of the downloaded content"
+            },
+            "status_code": {
+              "type": "integer",
+              "description": "HTTP status code"
+            }
+          }
+        },
+        {
+          "type": "object",
+          "description": "Returned content (when return_content=true)",
+          "properties": {
+            "content": {
+              "type": "string",
+              "description": "File content as text"
+            },
+            "content_type": {
+              "type": "string",
+              "description": "MIME type of the content"
+            },
+            "size": {
+              "type": "integer",
+              "description": "Size of content in characters"
+            },
+            "url": {
+              "type": "string",
+              "description": "Original URL"
+            }
+          }
+        },
+        {
+          "type": "object",
+          "description": "Error response",
+          "properties": {
+            "error": {
+              "type": "string",
+              "description": "Error message"
+            }
+          }
+        }
+      ]
+    }
+  },
+  {
+    "type": "BinaryDownloadTool",
+    "name": "download_binary_file",
+    "description": "Download binary files (images, videos, executables) with chunked streaming for better memory management. Optimized for large files.",
+    "fields": {
+      "return_key": "file_path"
+    },
+    "parameter": {
+      "type": "object",
+      "required": [
+        "url",
+        "output_path"
+      ],
+      "additionalProperties": false,
+      "properties": {
+        "url": {
+          "type": "string",
+          "description": "HTTP or HTTPS URL to download from",
+          "format": "uri"
+        },
+        "output_path": {
+          "type": "string",
+          "description": "Full path where to save the binary file (e.g., /tmp/image.jpg or C:\\Users\\Downloads\\video.mp4)",
+          "example": "/path/to/save/file.bin"
+        },
+        "chunk_size": {
+          "type": "integer",
+          "description": "Download chunk size in bytes (default: 1MB for binary files)",
+          "minimum": 1024,
+          "maximum": 10485760,
+          "default": 1048576
+        },
+        "timeout": {
+          "type": "integer",
+          "description": "Request timeout in seconds",
+          "minimum": 1,
+          "maximum": 300,
+          "default": 30
+        }
+      }
+    },
+    "return_schema": {
+      "oneOf": [
+        {
+          "type": "object",
+          "description": "Successfully downloaded binary file",
+          "properties": {
+            "file_path": {
+              "type": "string",
+              "description": "Absolute path to the downloaded file"
+            },
+            "size": {
+              "type": "integer",
+              "description": "Size of the file in bytes"
+            },
+            "content_type": {
+              "type": "string",
+              "description": "MIME type of the downloaded content"
+            },
+            "content_length": {
+              "type": "string",
+              "description": "Content-Length header value"
+            },
+            "url": {
+              "type": "string",
+              "description": "Original URL"
+            },
+            "status_code": {
+              "type": "integer",
+              "description": "HTTP status code"
+            }
+          }
+        },
+        {
+          "type": "object",
+          "description": "Error response",
+          "properties": {
+            "error": {
+              "type": "string",
+              "description": "Error message"
+            }
+          }
+        }
+      ]
+    }
+  },
+  {
+    "type": "TextDownloadTool",
+    "name": "download_text_content",
+    "description": "Download and return text content from URLs. Optimized for text files with automatic encoding detection.",
+    "fields": {
+      "return_key": "content"
+    },
+    "parameter": {
+      "type": "object",
+      "required": [
+        "url"
+      ],
+      "additionalProperties": false,
+      "properties": {
+        "url": {
+          "type": "string",
+          "description": "HTTP or HTTPS URL to download text from",
+          "format": "uri"
+        },
+        "encoding": {
+          "type": "string",
+          "description": "Text encoding (e.g., utf-8, latin1). Auto-detected if not specified.",
+          "example": "utf-8"
+        },
+        "timeout": {
+          "type": "integer",
+          "description": "Request timeout in seconds",
+          "minimum": 1,
+          "maximum": 300,
+          "default": 30
+        }
+      }
+    },
+    "return_schema": {
+      "oneOf": [
+        {
+          "type": "object",
+          "description": "Successfully downloaded text content",
+          "properties": {
+            "content": {
+              "type": "string",
+              "description": "Text content from the URL"
+            },
+            "encoding": {
+              "type": "string",
+              "description": "Detected or specified encoding"
+            },
+            "size": {
+              "type": "integer",
+              "description": "Size of content in characters"
+            },
+            "url": {
+              "type": "string",
+              "description": "Original URL"
+            },
+            "content_type": {
+              "type": "string",
+              "description": "MIME type of the content"
+            }
+          }
+        },
+        {
+          "type": "object",
+          "description": "Error response",
+          "properties": {
+            "error": {
+              "type": "string",
+              "description": "Error message"
+            }
+          }
+        }
+      ]
+    }
+  }
+]