datalad clone

Synopsis

datalad clone [-h] [-d DATASET] [-D DESCRIPTION] [--reckless
    [auto|ephemeral|shared-...]] [--version] SOURCE [PATH]

Description

Obtain a dataset (copy) from a URL or local directory

The purpose of this command is to obtain a new clone (copy) of a dataset and place it into a not-yet-existing or empty directory. As such CLONE provides a strict subset of the functionality offered by INSTALL. Only a single dataset can be obtained, and immediate recursive installation of subdatasets is not supported. However, once a (super)dataset is installed via CLONE, any content, including subdatasets can be obtained by a subsequent GET command.

Primary differences over a direct git clone call are 1) the automatic initialization of a dataset annex (pure Git repositories are equally supported); 2) automatic registration of the newly obtained dataset as a subdataset (submodule), if a parent dataset is specified; 3) support for additional resource identifiers (DataLad resource identifiers as used on datasets.datalad.org, and RIA store URLs as used for store.datalad.org - optionally in specific versions as identified by a branch or a tag; see examples); and 4) automatic configurable generation of alternative access URL for common cases (such as appending ‘.git’ to the URL in case the accessing the base URL failed).

In case the clone is registered as a subdataset, the original URL passed to CLONE is recorded in .GITMODULES of the parent dataset in addition to the resolved URL used internally for git-clone. This allows to preserve datalad specific URLs like ria+ssh://… for subsequent calls to GET if the subdataset was locally removed later on.

URL mapping configuration

‘clone’ supports the transformation of URLs via (multi-part) substitution specifications. A substitution specification is defined as a configuration setting ‘datalad.clone.url-substition.<seriesID>’ with a string containing a match and substitution expression, each following Python’s regular expression syntax. Both expressions are concatenated to a single string with an arbitrary delimiter character. The delimiter is defined by prefixing the string with the delimiter. Prefix and delimiter are stripped from the expressions (Example: “,^http://(.*)$,https://1”). This setting can be defined multiple times, using the same ‘<seriesID>’. Substitutions in a series will be applied incrementally, in order of their definition. The first substitution in such a series must match, otherwise no further substitutions in a series will be considered. However, following the first match all further substitutions in a series are processed, regardless whether intermediate expressions match or not. Substitution series themselves have no particular order, each matching series will result in a candidate clone URL. Consequently, the initial match specification in a series should be as precise as possible to prevent inflation of candidate URLs.

SEEALSO

handbook:3-001 (http://handbook.datalad.org/symbols)

More information on Remote Indexed Archive (RIA) stores

Examples

Install a dataset from Github into the current directory:

% datalad clone https://github.com/datalad-datasets/longnow-podcasts.git

Install a dataset into a specific directory:

% datalad clone https://github.com/datalad-datasets/longnow-podcasts.git \
  myfavpodcasts

Install a dataset as a subdataset into the current dataset:

% datalad clone -d . https://github.com/datalad-datasets/longnow-podcasts.git

Install the main superdataset from datasets.datalad.org:

% datalad clone ///

Install a dataset identified by a literal alias from store.datalad.org:

% datalad clone ria+http://store.datalad.org#~hcp-openaccess

Install a dataset in a specific version as identified by a branch or tag name from store.datalad.org:

% datalad clone ria+http://store.datalad.org#76b6ca66-36b1-11ea-a2e6-f0d5bf7b5561@myidentifier

Install a dataset with group-write access permissions:

% datalad clone http://example.com/dataset --reckless shared-group

Options

SOURCE

URL, DataLad resource identifier, local path or instance of dataset to be cloned. Constraints: value must be a string

PATH

path to clone into. If no PATH is provided a destination path will be derived from a source URL similar to git clone.

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

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

-d DATASET, --dataset DATASET

(parent) dataset to clone into. If given, the newly cloned dataset is registered as a subdataset of the parent. Also, if given, relative paths are interpreted as being relative to the parent dataset, and not relative to the working directory. Constraints: Value must be a Dataset or a valid identifier of a Dataset (e.g. a path)

-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

--reckless [auto|ephemeral|shared-…]

set up the dataset 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’. 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. Please note, that this is meant to be used with either non-bare repositories or a RIA store as origin! Do not come up with your own usecase unless you are absolutely sure you know your git-annex internals very well! [‘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-’

--version

show the module and its version which provides the command

Authors

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