| description = [ |
| { |
| "description": "Executes the provided Python command in the notebook environment and returns the output.", |
| "name": "run_python_repl", |
| "optional_parameters": [], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "Python command to execute in the notebook environment", |
| "name": "command", |
| "type": "str", |
| } |
| ], |
| }, |
| { |
| "description": "Read the source code of a function from any module path.", |
| "name": "read_function_source_code", |
| "optional_parameters": [], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "Fully qualified function name " |
| "(e.g., " |
| "'bioagentos.tool.support_tools.write_python_code')", |
| "name": "function_name", |
| "type": "str", |
| } |
| ], |
| }, |
| { |
| "description": "Download data from Synapse using entity IDs. Requires SYNAPSE_AUTH_TOKEN environment variable for authentication. CRITICAL: Always specify entity_type parameter based on what you're downloading (file, dataset, folder, project). Check user hints like 'files' or search results to determine correct type. Multiple IDs only work with entity_type='file'. Recursive only works with entity_type='folder'.", |
| "name": "download_synapse_data", |
| "optional_parameters": [ |
| { |
| "name": "download_location", |
| "type": "str", |
| "description": "Directory where files will be downloaded", |
| "default": ".", |
| }, |
| { |
| "name": "follow_link", |
| "type": "bool", |
| "description": "Whether to follow links to download the linked entity", |
| "default": False, |
| }, |
| { |
| "name": "recursive", |
| "type": "bool", |
| "description": "Whether to recursively download folders and their contents. ONLY valid with entity_type='folder'", |
| "default": False, |
| }, |
| { |
| "name": "timeout", |
| "type": "int", |
| "description": "Timeout in seconds for each download operation", |
| "default": 300, |
| }, |
| { |
| "name": "entity_type", |
| "type": "str", |
| "description": "Type of Synapse entity: 'file', 'dataset', 'folder', or 'project'. MUST match actual entity type! Check user hints (e.g., 'files' means entity_type='file') or search results ('node_type' field). Default 'dataset' should only be used for actual datasets.", |
| "default": "dataset", |
| }, |
| ], |
| "required_parameters": [ |
| { |
| "name": "entity_ids", |
| "type": "str|list[str]", |
| "description": "Synapse entity ID(s) to download. For files: single ID or list of IDs. For datasets/folders/projects: single ID only", |
| "default": None, |
| } |
| ], |
| }, |
| ] |
|
|
