tooluniverse.gene_ontology_tool module

tooluniverse.gene_ontology_tool.quote('abc def') → 'abc%20def'

Each part of a URL, e.g. the path info, the query, etc., has a different set of reserved characters that must be quoted. The quote function offers a cautious (not minimal) way to quote a string for most of these parts.

RFC 3986 Uniform Resource Identifier (URI): Generic Syntax lists the following (un)reserved characters.

unreserved = ALPHA / DIGIT / “-” / “.” / “_” / “~” reserved = gen-delims / sub-delims gen-delims = “:” / “/” / “?” / “#” / “[” / “]” / “@” sub-delims = “!” / “$” / “&” / “’” / “(” / “)”

/ “*” / “+” / “,” / “;” / “=”

Each of the reserved characters is reserved in some component of a URL, but not necessarily in all of them.

The quote function %-escapes all characters that are neither in the unreserved chars (“always safe”) nor the additional chars set via the safe arg.

The default for the safe arg is ‘/’. The character is reserved, but in typical usage the quote function is being called on a path where the existing slash characters are to be preserved.

Python 3.7 updates from using RFC 2396 to RFC 3986 to quote URL strings. Now, “~” is included in the set of unreserved characters.

string and safe may be either str or bytes objects. encoding and errors must not be specified if string is a bytes object.

The optional encoding and errors parameters specify how to deal with non-ASCII characters, as accepted by the str.encode method. By default, encoding=’utf-8’ (characters are encoded with UTF-8), and errors=’strict’ (unsupported characters raise a UnicodeEncodeError).

class tooluniverse.gene_ontology_tool.BaseTool(tool_config)

Bases: object

__init__(tool_config)

classmethod get_default_config_file()

Get the path to the default configuration file for this tool type.

This method uses a robust path resolution strategy that works across different installation scenarios:

1. Installed packages: Uses importlib.resources for proper package resource access

2. Development mode: Falls back to file-based path resolution

3. Legacy Python: Handles importlib.resources and importlib_resources

Override this method in subclasses to specify a custom defaults file.

Returns:

Path or resource object pointing to the defaults file

classmethod load_defaults_from_file()

Load defaults from the configuration file

run(arguments=None)

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.

check_function_call(function_call_json)

get_required_parameters()

Retrieve required parameters from the endpoint definition. Returns: list: List of required parameters for the given endpoint.

tooluniverse.gene_ontology_tool.register_tool(tool_type_name=None, config=None)

Decorator to automatically register tool classes and their configs.

Usage:

@register_tool(‘CustomToolName’, config={…}) class MyTool:

pass

class tooluniverse.gene_ontology_tool.GeneOntologyTool(tool_config: Dict)

Bases: BaseTool

A general-purpose tool for calling the Gene Ontology (GO) API. It is configured via a dictionary that defines the specific API endpoint.

__init__(tool_config: Dict)

Initializes the tool with a configuration.

Parameters:

tool_config (Dict) – A dictionary containing ‘fields’ with an ‘endpoint’.

run(arguments: Any | None = None) → Any

Executes the API call and returns the data.

Parameters:

arguments (Dict[str, Any]) – Parameters for the API call.

Returns:

The JSON data from the API or an error dictionary.

Return type:

Any

search_terms(query: str) → Any

get_term_details(id: str) → Any

get_genes_for_term(id: str, taxon: str | None = None, rows: int | None = None) → Any

get_terms_for_gene(id: str) → Any