datalad.api.ukb_update

datalad.api.ukb_update(keyfile=None, merge=False, force=False, drop=None, dataset=None)

Update an existing dataset of a UKbiobank participant

This command expects an ukb-init initialized DataLad dataset. The dataset may or may not have any downloaded content already.

Downloads are performed with the ukbfetch tool, which is expected to be available and executable.

Parameters:
  • keyfile (str or None, optional) – path to a file with an authentification key (ukbfetch -a …). If none is given, the configuration datalad.ukbiobank.keyfile is consulted. [Default: None]
  • merge (bool, optional) – merge any updates into the active branch. If a BIDS layout is maintained in the dataset (incoming-bids branch) it will be merged into the active branch, the incoming-native branch otherwise. [Default: False]
  • force (bool, optional) – update the incoming branch(es), even if (re-)download did not yield changed content (can be useful when restructuring setup has changed). [Default: False]
  • drop ({None, 'extracted', 'archives'}, optional) – Drop file content to avoid storage duplication. ‘extracted’: drop all content of files extracted from downloaded archives to yield the most compact storage at the cost of partial re-extraction when accessing archive content; ‘archives’: keep extracted content, but drop archives instead. By default no content is dropped, duplicating archive content in extracted form. [Default: None]
  • 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 ({'default', 'json', 'json_pp', 'tailored'} or None, optional) – format of return value rendering on stdout. [Default: None]
  • 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’]