datalad.api.ukb_init(participant, records, force=False, bids=False, dataset=None)

Initialize an existing dataset to track a UKBiobank participant

A batch file for the ‘ukbfetch’ tool will be generated and placed into the dataset. By selecting the relevant data records, raw and/or preprocessed data will be tracked.

After initialization the dataset will contain at least three branches:

  • ‘incoming’: to track the pristine ZIP files downloaded from UKB
  • ‘incoming-native’: to track individual files (some extracted from ZIP files)
  • ‘incoming-bids’: to track individual files in a layout where file name conform to BIDS-conventions
  • main branch: based off of incoming-native or incoming-bids (if enabled) with potential manual modifications applied


Initialize a dataset in the current directory:

> ukb_init(participant="5874415", records=["20227_2_0", "20249_2_0"])

Initialize a dataset in the current directory in BIDS layout:

> ukb_init(participant="5874415", records=["20227_2_0"], bids=True)
  • participant (1-item sequence of str) – UKBiobank participant ID to use for this dataset (note: these encoded IDs are unique to each application/project).
  • records (non-empty sequence of str) – One or more data record identifiers.
  • force (bool, optional) – force (re-)initialization. [Default: False]
  • bids (bool, optional) – additionally maintain an incoming-bids branch with a BIDS-like organization. [Default: False]
  • dataset (Dataset or None, optional) – specify the dataset to perform the initialization on. [Default: None]
  • on_failure ({'ignore', 'continue', 'stop'}, optional) – behavior to perform on failure: ‘ignore’ any failure is reported, but does not cause an exception; ‘continue’ if any failure occurs an exception will be raised at the end, but processing other actions will continue for as long as possible; ‘stop’: processing will stop on first failure and an exception is raised. A failure is any result with status ‘impossible’ or ‘error’. Raised exception is an IncompleteResultsError that carries the result dictionaries of the failures in its failed attribute. [Default: ‘continue’]
  • result_filter (callable or None, optional) – if given, each to-be-returned status dictionary is passed to this callable, and is only returned if the callable’s return value does not evaluate to False or a ValueError exception is raised. If the given callable supports **kwargs it will additionally be passed the keyword arguments of the original API call. [Default: None]
  • result_renderer – select rendering mode command results. ‘tailored’ enables a command- specific rendering style that is typically tailored to human consumption, if there is one for a specific command, or otherwise falls back on the the ‘generic’ result renderer; ‘generic’ renders each result in one line with key info like action, status, path, and an optional message); ‘json’ a complete JSON line serialization of the full result record; ‘json_pp’ like ‘json’, but pretty-printed spanning multiple lines; ‘disabled’ turns off result rendering entirely; ‘<template>’ reports any value(s) of any result properties in any format indicated by the template (e.g. ‘{path}’, compare with JSON output for all key-value choices). The template syntax follows the Python “format() language”. It is possible to report individual dictionary values, e.g. ‘{metadata[name]}’. If a 2nd-level key contains a colon, e.g. ‘music:Genre’, ‘:’ must be substituted by ‘#’ in the template, like so: ‘{metadata[music#Genre]}’. [Default: ‘tailored’]
  • result_xfm ({'datasets', 'successdatasets-or-none', 'paths', 'relpaths', 'metadata'} or callable or None, optional) – if given, each to-be-returned result status dictionary is passed to this callable, and its return value becomes the result instead. This is different from result_filter, as it can perform arbitrary transformation of the result value. This is mostly useful for top- level command invocations that need to provide the results in a particular format. Instead of a callable, a label for a pre-crafted result transformation can be given. [Default: None]
  • return_type ({'generator', 'list', 'item-or-list'}, optional) – return value behavior switch. If ‘item-or-list’ a single value is returned instead of a one-item return value list, or a list in case of multiple return values. None is return in case of an empty list. [Default: ‘list’]