Man page - datalad-get(1)

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Manual

datalad get

NAME
SYNOPSIS
DESCRIPTION
Getting subdatasets
Examples
OPTIONS
AUTHORS

NAME

datalad get - get any dataset content (files/directories/subdatasets).

SYNOPSIS

datalad get [-h] [-s LABEL] [-d PATH] [-r] [-R LEVELS] [-n] [-D DESCRIPTION] [--reckless [auto|ephemeral|shared-...]] [-J NJOBS] [--version] [PATH ...]

DESCRIPTION

This command only operates on dataset content. To obtain a new independent dataset from some source use the CLONE command.

By default this command operates recursively within a dataset, but not across potential subdatasets, i.e. if a directory is provided, all files in the directory are obtained. Recursion into subdatasets is supported too. If enabled, relevant subdatasets are detected and installed in order to fulfill a request.

Known data locations for each requested file are evaluated and data are obtained from some available location (according to git-annex configuration and possibly assigned remote priorities), unless a specific source is specified.

Getting subdatasets

Just as DataLad supports getting file content from more than one location, the same is supported for subdatasets, including a ranking of individual sources for prioritization.

The following location candidates are considered. For each candidate a cost is given in parenthesis, higher values indicate higher cost, and thus lower priority:

- A datalad URL recorded in ‘.gitmodules‘ (cost 590). This allows for datalad URLs that require additional handling/resolution by datalad, like ria-schemes (ria+http, ria+ssh, etc.)

- A URL or absolute path recorded for git in ‘.gitmodules‘ (cost 600).

- URL of any configured superdataset remote that is known to have the desired submodule commit, with the submodule path appended to it. There can be more than one candidate (cost 650).

- In case ‘.gitmodules‘ contains a relative path instead of a URL, the URL of any configured superdataset remote that is known to have the desired submodule commit, with this relative path appended to it. There can be more than one candidate (cost 650).

- In case ‘.gitmodules‘ contains a relative path as a URL, the absolute path of the superdataset, appended with this relative path (cost 900).

Additional candidate URLs can be generated based on templates specified as configuration variables with the pattern

‘datalad.get.subdataset-source-candidate-<name>‘

where NAME is an arbitrary identifier. If ‘name‘ starts with three digits (e.g. ’400myserver’) these will be interpreted as a cost, and the respective candidate will be sorted into the generated candidate list according to this cost. If no cost is given, a default of 700 is used.

A template string assigned to such a variable can utilize the Python format mini language and may reference a number of properties that are inferred from the parent dataset’s knowledge about the target subdataset. Properties include any submodule property specified in the respective ‘.gitmodules‘ record. For convenience, an existing ‘datalad-id‘ record is made available under the shortened name ID.

Additionally, the URL of any configured remote that contains the respective submodule commit is available as ‘remoteurl-<name>‘ property, where NAME is the configured remote name.

Hence, such a template could be ‘http://example.org/datasets/{id}‘ or ‘http://example.org/datasets/{path}‘, where ‘{id}‘ and ‘{path}‘ would be replaced by the ‘datalad-id‘ or PATH entry in the ‘.gitmodules‘ record.

If this config is committed in ‘.datalad/config‘, a clone of a dataset can look up any subdataset’s URL according to such scheme(s) irrespective of what URL is recorded in ‘.gitmodules‘.

Lastly, all candidates are sorted according to their cost (lower values first), and duplicate URLs are stripped, while preserving the first item in the candidate list.

NOTE

Power-user info: This command uses git annex get to fulfill file handles.

Examples

Get a single file::

% datalad get <path/to/file>

Get contents of a directory::

% datalad get <path/to/dir/>

Get all contents of the current dataset and its subdatasets::

% datalad get . -r

Get (clone) a registered subdataset, but don’t retrieve data::

% datalad get -n <path/to/subds>

OPTIONS

PATH

path/name of the requested dataset component. The component must already be known to a dataset. To add new components to a dataset use the ADD command. Constraints: value must be a string or value must be NONE

-h , --help , --help-np

show this help message. --help-np forcefully disables the use of a pager for displaying the help message

-s LABEL, --source LABEL

label of the data source to be used to fulfill requests. This can be the name of a dataset sibling or another known source. Constraints: value must be a string or value must be NONE

-d PATH, --dataset PATH

specify the dataset to perform the add operation on, in which case PATH arguments are interpreted as being relative to this dataset. If no dataset is given, an attempt is made to identify a dataset for each input ‘path‘. Constraints: Value must be a Dataset or a valid identifier of a Dataset (e.g. a path) or value must be NONE

-r , --recursive

if set, recurse into potential subdatasets.

-R LEVELS, --recursion-limit LEVELS

limit recursion into subdataset to the given number of levels. Alternatively, ’existing’ will limit recursion to subdatasets that already existed on the filesystem at the start of processing, and prevent new subdatasets from being obtained recursively. Constraints: value must be convertible to type ’int’ or value must be one of (’existing’,) or value must be NONE

-n , --no-data

whether to obtain data for all file handles. If disabled, GET operations are limited to dataset handles. This option prevents data for file handles from being obtained.

-D DESCRIPTION , --description DESCRIPTION

short description to use for a dataset location. Its primary purpose is to help humans to identify a dataset copy (e.g., "mike’s dataset on lab server"). Note that when a dataset is published, this information becomes available on the remote side. Constraints: value must be a string or value must be NONE

--reckless [auto|ephemeral|shared-...]

Obtain a dataset or subdatset and set it up in a potentially unsafe way for performance, or access reasons. Use with care, any dataset is marked as ’untrusted’. The reckless mode is stored in a dataset’s local configuration under ’datalad.clone.reckless’, and will be inherited to any of its subdatasets. Supported modes are: [’auto’]: hard-link files between local clones. In-place modification in any clone will alter original annex content. [’ephemeral’]: symlink annex to origin’s annex and discard local availability info via git-annex-dead ’here’ and declares this annex private. Shares an annex between origin and clone w/o git-annex being aware of it. In case of a change in origin you need to update the clone before you’re able to save new content on your end. Alternative to ’auto’ when hardlinks are not an option, or number of consumed inodes needs to be minimized. Note that this mode can only be used with clones from non-bare repositories or a RIA store! Otherwise two different annex object tree structures (dirhashmixed vs dirhashlower) will be used simultaneously, and annex keys using the respective other structure will be inaccessible. [’shared-<mode>’]: set up repository and annex permission to enable multi-user access. This disables the standard write protection of annex’ed files. <mode> can be any value support by ’git init --shared=’, such as ’group’, or ’all’. Constraints: value must be one of (True, False, ’auto’, ’ephemeral’) or value must start with ’shared-’

-J NJOBS, --jobs NJOBS

how many parallel jobs (where possible) to use. "auto" corresponds to the number defined by ’datalad.runtime.max-annex-jobs’ configuration item NOTE: This option can only parallelize input retrieval (get) and output recording (save). DataLad does NOT parallelize your scripts for you. Constraints: value must be convertible to type ’int’ or value must be NONE or value must be one of (’auto’,) [Default: ’auto’]

--version

show the module and its version which provides the command

AUTHORS

datalad is developed by The DataLad Team and Contributors <team@datalad.org>.