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deposits

The deposits R package is a universal client for depositing and accessing research data anywhere. Currently supported services are zenodo and figshare. This README primarily contains information on setting up the deposits package. Use of the package is described in the introductory vignette.

Installation

The package can be installed by enabling the “ropensci” r-universe, and using install.packages():

options (repos = c (
    ropensci = "https://ropensci.r-universe.dev",
    CRAN = "https://cloud.r-project.org"
))
install.packages ("deposits")

Alternatively, the package can be installed directly from GitHub with the following command:

remotes::install_github ("ropenscilabs/deposits")

The package can then be loaded for use with:

Data Repositories

The list of data repositories currently supported is accessible by the deposits_services() function:

##             name                           docs                    api_base_url
## 1         zenodo https://developers.zenodo.org/         https://zenodo.org/api/
## 2 zenodo-sandbox https://developers.zenodo.org/ https://sandbox.zenodo.org/api/
## 3       figshare     https://docs.figshare.com/    https://api.figshare.com/v2/

zenodo offers a “sandbox” environment, which offers an ideal environment for testing the functionality of this package.

API tokens

All services require users to create an account and then to generate API (“Application Programming Interface”) tokens. Click on the following links to generate tokens, also listed as sequences of menu items used to reach token settings:

It is not necessary to create or register applications on any of these services; this package uses personal tokens only. The tokens need to be stored as local environment variables the names of which must include the names of the respective services, as defined by the “name” column returned from deposits_service(), as shown above. This can be done as in the following example:

Sys.setenv ("ZENODO_SANDBOX_TOKEN" = "<my-token")

Alternatively, these tokens can be stored in a ~/.Renviron file, where they will be automatically loaded into every R session.

Functionality

The deposits package extends from an R6 client offering a variety of methods for performing actions on deposits services. Details of the methods can be seen in the help file for the depositsClient. All deposits operations start with a client constructed with the new() function, with a first parameter specifying the desired deposits service:

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 command, ls(cli), will list all elements of the R6 object, with the functions prefixed with deposit_ or deposits_. These functions are:

  1. deposit_delete(deposit_id) to delete a nominated deposit;
  2. deposit_download_file(deposit_id, filename) to download nominated filename from specified deposit.
  3. deposit_fill_metadata(meta) to fill a deposits client with metadata (see introductory vignette for details);
  4. deposit_new() to create a new deposit on a deposits service using the metadata inserted with fill_metadata();
  5. deposit_retrieve(deposit_id) to retrieve information on a specified deposit;
  6. deposit_update(deposit_id) to update deposit on server with local metadata;
  7. deposit_upload_file(deposit_id, path) to upload a local file to a specified deposit; and
  8. deposits_list() to update lists of current deposits within client.

An introductory vignette demonstrates all of these functions, while the “Metadata” vignette describes processes to specify deposit metadata with a deposits client.

Code of Conduct

Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.