tooluniverse.pubtator_tool module

class tooluniverse.pubtator_tool.PubTatorTool(tool_config: Dict[str, Any])

Bases: BaseTool

Generic wrapper around a single PubTator 3 endpoint supporting JSON-defined configs.

__init__(tool_config: Dict[str, Any])

_compose_url(args: Dict[str, Any]) → str

Substitute template vars & build full URL.

_filter_search_results(result: Dict[str, Any]) → Dict[str, Any]

Filter PubTatorSearch results by score threshold and remove facet items that only have ‘name’, ‘type’, and ‘value’.

_query_params(args: Dict[str, Any]) → Dict[str, str]

Translate caller arg names → API param names, drop Nones, serialise lists.

run(arguments: Dict[str, Any])

Execute the tool.

The default BaseTool implementation accepts an optional arguments mapping to align with most concrete tool implementations which expect a dictionary of inputs.