Engineering and extensions: 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.

ENCODE returns text: mostly JSON, but get_citations can return BibTeX/RIS and export_data can return CSV/TSV. Use json.loads() only for JSON. Tracking and credentials use ~/.dnakit-encode/; persistent credential storage needs dnakit[encode-credentials].

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.

Read cells and outputs from an executed notebook

dnakit.databases.read_executed_notebook(*, data_folder=None, notebook_path=None, search=None, regex=None, max_output_chars=None, include_source=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
data_folder	string | null	None	Directory to search (recursively) for a .ipynb file. Prefers *_executed.ipynb over regular .ipynb. Provide either this OR notebook_path.
notebook_path	string | null	None	Direct path to a specific .ipynb file. Provide either this OR data_folder.
search	string	None	Optional: comma-separated terms (or regex if regex=true). Cells whose source or output contains any term are returned in 'matching_cells'. Case-insensitive. Example: 'upregulated,log2FoldChange' or 'padj.*0.05'
regex	boolean	None	Treat 'search' as a Python regex instead of a comma-separated term list (default: false)
max_output_chars	integer	None	Truncate each cell source/output to this many characters (default 400)
include_source	boolean	None	Include cell source code in the response (default true). Set false to halve response size when you only need outputs.
verbose	bool	True	Progress flag.

Manage ENCODE API credentials

dnakit.encode.manage_credentials(action, access_key=None, secret_key=None, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
action	Literal['store', 'check', 'clear']	Required	What to do: - "store": Save new credentials (requires access_key and secret_key) - "check": Check if credentials are configured - "clear": Remove stored credentials
access_key	str | None	None	Your ENCODE access key (only for action="store")
secret_key	str | None	None	Your ENCODE secret key (only for action="store")
verbose	bool	True	Show DNAKit progress messages without changing results.

Locate and verify a bundled resource file

dnakit.workflows.resource_path(skill_id, resource, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
skill_id	str	Required	Bundled skill ID or registered legacy alias.
resource	str	Required	Relative resource path within the skill; verified before use.
verbose	bool	True	Show DNAKit progress messages without changing results.

Run a bundled workflow and retrieve its exit code and output

dnakit.workflows.run(skill_id, script, *, arguments=None, workdir=None, timeout_seconds=300.0, max_output_bytes=1000000, verbose=True)

Parameter	Type	Required / default	Description and constraints
skill_id	str	Required	Bundled skill ID or registered legacy alias.
script	str	Required	Relative .py, .R or .sh script path inside the bundle.
arguments	list[str] | None	None	Parameter mapping for database calls; CLI string list for workflows.
workdir	str | Path | None	None	Subprocess working directory; None uses the current directory.
timeout_seconds	float	300.0	Subprocess timeout in seconds.
max_output_bytes	int	1000000	Maximum captured subprocess output bytes.
verbose	bool	True	Show DNAKit progress messages without changing results.

Run a support script for a composite workflow

dnakit.workflows.run_support(name, *, arguments=None, workdir=None, timeout_seconds=300, max_output_bytes=1000000, verbose=True)

Parameter	Type	Required / default	Description and constraints
name	str	Required	Support workflow name; allowed values are described below.
arguments	list[str] | None	None	Parameter mapping for database calls; CLI string list for workflows.
workdir	str | Path | None	None	Subprocess working directory; None uses the current directory.
timeout_seconds	float	300	Subprocess timeout in seconds.
max_output_bytes	int	1000000	Maximum captured subprocess output bytes.
verbose	bool	True	Show DNAKit progress messages without changing results.

List bundled Python, R and shell scripts

dnakit.workflows.scripts(skill_id, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
skill_id	str	Required	Bundled skill ID or registered legacy alias.
verbose	bool	True	Show DNAKit progress messages without changing results.

Render an existing Markdown report as a PDF

dnakit.workflows.write_wes_report(input_report, output_dir, *, language='en', title=None, logo_left=None, logo_right=None, font_path=None, overwrite=False, verbose=True)

Parameter	Type	Required / default	Description and constraints
input_report	str | Path	Required	Existing UTF-8 Markdown report path, at most 5 MB.
output_dir	str | Path	Required	Report output directory for the PDF and provenance manifest.
language	str	'en'	Report label language en or es; input text is not translated.
title	str | None	None	Custom report title; None uses the language default.
logo_left	str | Path | None	None	Left logo image path.
logo_right	str | Path | None	None	Right logo image path.
font_path	str | Path | None	None	Optional TTF font path.
overwrite	bool	False	Allow overwriting existing report files.
verbose	bool	True	Show DNAKit progress messages without changing results.