tooluniverse.pubtator_tool module

class tooluniverse.pubtator_tool.PubTatorTool

Bases: BaseTool

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

__init__(tool_config)

run(arguments)

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.

Parameters:

• arguments (dict, optional) – Tool-specific arguments

• stream_callback (callable, optional) – Callback for streaming responses

• use_cache (bool, optional) – Whether result caching is enabled

• validate (bool, optional) – Whether parameter validation was performed

Note

These additional parameters (stream_callback, use_cache, validate) are passed from run_one_function() to provide context about the execution. Tools can use these for optimization or special handling.

For backward compatibility, tools that don’t accept these parameters will still work - they will only receive the arguments parameter.

_compose_url(args)

Substitute template vars & build full URL.

_query_params(args)

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

_filter_search_results(result)

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