Discover and call database APIs: parameters and notes¶

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

scripts, resource_path, describe, search and list_operations support local discovery or resource reads. run and run_support execute scripts which may access networks or write files; prepare their interpreters, scientific software and reference data. The existing strict YAML run_workflow is separate from these script runners.

Call a database operation by name and parameters¶

dnakit.databases.call(operation, arguments=None, *, max_result_bytes=20000000, verbose=True)

Parameter	Type	Required / default	Description and constraints
`operation`	str	Required	Native operation name or registered upstream alias.
`arguments`	Mapping[str, object] \| None	None	Parameter mapping for database calls; CLI string list for workflows.
`max_result_bytes`	int	20000000	Serialized result byte limit; exceeding it raises an exception.
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Inspect database input schemas and provenance¶

dnakit.databases.describe(operation, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`operation`	str	Required	Native operation name or registered upstream alias.
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Execute a structured database request¶

dnakit.databases.execute(request, arguments=None, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`request`	str \| Mapping[str, object]	Required	Operation name or a mapping with name and arguments.
`arguments`	Mapping[str, object] \| None	None	Parameter mapping for database calls; CLI string list for workflows.
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Dispatch a database operation using a compatible tool name¶

dnakit.databases.execute_tool(*, tool_name, arguments=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
`tool_name`	string	Required	Name of the tool to execute (e.g., 'example_tool_name')
`arguments`	object \| None	None	Tool arguments as either (1) a JSON object dictionary or (2) a JSON string that decodes to an object. Object example: {"param1": "value1", "param2": 5}. JSON string example: "{\"param1\": \"value1\", \"param2\": 5}". {"oneOf": [{"type": "object", "additionalProperties": true}, {"type": "string"}]}
`verbose`	bool	True	Progress flag.

List database operations and aliases offline¶

dnakit.databases.list_operations(*, verbose=True)

Parameter	Type	Required / default	Description and constraints
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Discover database operations by task keywords offline¶

dnakit.databases.search(query, *, limit=10, verbose=True)

Parameter	Type	Required / default	Description and constraints
`query`	str	Required	Local name/description search; use English task terms or a function name.
`limit`	int	10	Maximum matches; database catalog search allows 1–100.
`verbose`	bool	True	Show DNAKit progress messages without changing results.