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.

  • 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 – 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’]