datalad.api.xnat_init

datalad.api.xnat_init(url, pathfmt='{subject}/{session}/{scan}/', project=None, subject=None, experiment=None, collection=None, credential=None, force=False, interactive=None, dataset=None)

Initialize an existing dataset to track an XNAT project

Examples

Initialize a dataset in the current directory:

> xnat_init("http://central.xnat.org:8080")

Initialize with anonymous access (no credentials used):

> xnat_init("https://central.xnat.org", credential="anonymous")

Use credentials previously stored as <NAME>:

> xnat_init("https://central.xnat.org", credential="<NAME>")

Track a specific XNAT project, without credentials:

> xnat_init("https://central.xnat.org", project="Sample_DICOM", credential="anonymous")
Parameters:

  • url -- XNAT instance URL.

  • pathfmt -- Specify the directory structure for the downloaded files, and if/where a subdataset should be created. The format string must use POSIX notation and must end with a slash ('/'). To include the subject, session, or scan values, use the following format: {subject}/{session}/{scan}/ To insert a subdataset at a specific directory level use '//': {subject}/{session}//{scan}/. [Default: '{subject}/{session}/{scan}/']

  • project -- accession ID of a single XNAT project to track. [Default: None]

  • subject -- accession ID of a single subject to track. [Default: None]

  • experiment -- accession ID of a single experiment to track. [Default: None]

  • collection -- limit updates to a specific collection/resource. Multiple collections can be specified as a list. [Default: None]

  • credential (str or None, optional) -- name of the credential providing a user/password combination to be used for authentication. The special value 'anonymous' will cause no credentials to be used, and all XNAT requests to be performed anonymously. The credential can be supplied via configuration settings 'datalad.credential.<name>.{user|password}', or environment variables DATALAD_CREDENTIAL_<NAME>_{USER|PASSWORD}, or will be queried from the active credential store using the provided name. If none is provided, the host-part of the XNAT URL is used as a name (e.g. 'https://central.xnat.org' -> 'central.xnat.org'). [Default: None]

  • force (bool, optional) -- force (re-)initialization. [Default: False]

  • interactive (bool, optional) -- enables interactive configuration based on XNAT queries. Default: enabled in interactive sessions. [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']