In ropenscilabs/deposits: A universal client for depositing and accessing research data anywhere

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The deposits package uses an R6 client to interface with the individual deposition services. This vignette briefly explains explains the properties of a deposits client for those unfamiliar with R6 objects.

R6 methods

The R6 package used to construct deposits clients here allows for structured class objects in R. The objects include elements (such as variables) and methods, which for R are generally functions. A new client can be constructed with the new operator, which for deposits requires specifying the service for which the client is to be constructed:

library (deposits)
cli <- depositsClient$new (service = "figshare")

Additional functions are called in a similar way, using a $-notation, in the form cli$deposit_function(). The deposits package is constructed so that function calls constructed is this way will "automatically" update the object itself, and so generally do not need to be assigned to a return value. For example, the function deposits_list() updates the list of deposits on the associated service. In conventional R packages, calling this function would require assigning a return value like this:

cli_updated <- cli$deposits_list ()

R6 objects are, however, always updated internally, so the client itself, cli, will already include the updated list of deposits without any need for assigning the return value to cli_updated. That is, rather than the above line, all deposits functions may be called simply as,

cli$deposits_list ()

(The single exception to this is the deposit_download_file() function, which returns the path to the locally downloaded file, and so should always be assigned to a return value.)

Initialising a deposits client

An empty client can be constructed by naming the desired service. An additional sandbox parameter constructs a client to the zenodo sandbox environment intended for testing their API. Actual use of the zenodo API can then be enabled with the default sandbox = FALSE.

cli <- depositsClient$new ("zenodo", sandbox = TRUE)
cli
#> <deposits client>
#> deposits service : zenodo
#>           sandbox: TRUE
#>         url_base : https://sandbox.zenodo.org/api/
#> Current deposits : <none>
#>
#>   hostdata : <none>
#>   metadata : <none>

The R6 client structure

All R6 clients share a few build-in methods which can be used to understand their internal structure and functionality. In particular, both the ls() and str() functions reveal internal details of R6 clients. These details are nevertheless not particularly helpful here, and the deposits client has it's own deposits_methods() function intended to provide an overview all all implemented methods:

cli$deposits_methods ()
#> List of methods for a deposits client:
#>
#>    - deposit_add_resource
#>    - deposit_delete
#>    - deposit_delete_file
#>    - deposit_download_file
#>    - deposit_embargo
#>    - deposit_fill_metadata
#>    - deposit_new
#>    - deposit_prereserve_doi
#>    - deposit_publish
#>    - deposit_retrieve
#>    - deposit_service
#>    - deposit_update
#>    - deposit_upload_file
#>    - deposit_version
#>    - deposits_list
#>    - deposits_methods
#>    - deposits_search
#>
#>  see `?depositsClient` for full details of all methods.

As described in the final line of that output, the documentation contains full details of all methods, also provided in the online documentation.

ropenscilabs/deposits documentation built on July 16, 2025, 1:38 p.m.