A universal client for depositing and accessing research data anywhere • deposits

The deposits R package is a universal client for depositing and accessing research data anywhere. Currently supported services are zenodo and figshare. The package works seamlessly with the “frictionless” data workflow. Instructions for installing and setting up the package are in a separate vignette. This README gives a brief overview of package usage, with more detail in the introductory vignette.

Data Repositories

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

library (deposits)
deposits_services ()

##             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/

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

The “frictionless” data workflow

Prior to describing the deposits workflow, it is useful to understand the “frictionless” data workflow, which provides a standardised way to document the contents and structure of data files through a separate metadata file. The deposits package links directly with rOpenSci’s frictionless package for writing, editing, and reading frictionless metadata files.

The deposits package nevertheless aims to make this integration as seamless and painless as possible. No knowledge of the frictionless workflow is necessary, and the deposits workflow should “just work” in many cases, appropriately constructing frictionless metadata files and uploading them to deposits services. It is of course also possible to use the deposits package without frictionless metadata.

The deposits workflow

The deposits package uses the R6 package to create a depositsClient used to perform all functions. All deposits operations start with a client constructed with the new() function:

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

The upper section of information shown by printing the client describes information on the client in general, and aspects of the nominated service associated with the user (identified through the token, as described in the “Installation and Setup” vignette). The lower section contains information on the current deposit held within the client. A new client initially contains no information on a deposit, and so these lower sections are empty.

The code above demonstrates how R6 objects work, through calling “methods” or functions on the main “object” via the $ symbol. The “new” method must be called on a depositsClient object. From that point on, all other methods are called on that object itself. For example, the following calls lists all methods implemented by the client:

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

All of those methods then work similarly, by calling cli$<method>(<parameters>). Note that R6 functions are called directly on the client, with the object itself (cli) updated by the call. For example, the deposit_fil_metadata() method described below can be used to specify metadata for a deposit. This works by simply calling,

cli$deposit_fill_metadata (metadata)

The cli object is then updated by this call, without needing to be assigned to a return value (like cli <- cli$<method>).

A typical deposits workflow, and associated methods, involves the following steps:

Fill the client with metadata (using the new() or deposit_fill_metadata() methods);
Create a new deposit on the nominated service (using the deposit_new() method); and
Upload files for the deposit (using the deposit_upload_file() method).

The following sections describe each of these steps in more detail.

Fill client with metadata

The metadata of a deposit describe the nature and properties of the data being deposited. A deposit is first created by uploading metadata to a deposits service; only then can actual data be uploaded and associated with the deposit described by the metadata. The deposits package works with two main types of metadata:

Metadata which describe a deposit and associated properties, such as author names and affiliations, deposit titles and descriptions, dates, keywords, links to other deposits or publications, and many other terms.
Metadata which describe the actual contents of the data to be deposited. These kinds of metadata are (optionally) generated and (always) handled here by the frictionless package.

As explained at the outset, the deposits package can be used without knowing or understanding anything about the frictionless package or frictionless workflows. Most of this present section therefore concerns the first of these two kinds of metadata, with brief demonstrations of the second kind used to illustrate how the frictionless workflow integrates with the general deposits workflow. The term “metadata” throughout the following should be understood to refer to the first of the above kinds of metadata; the second kind is always referred to here as “frictionless metadata.”

Metadata can be included in a deposits client in two main ways, either on initial construction, or through attaching metadata to an existing client. One of the easiest of specifying metadata is as a list of named terms like the following example:

metadata <- list (
    title = "New Title",
    abstract = "This is the abstract",
    creator = list ("A. Person", "B. Person")
)

These data can be used in construction of a new client by passing a metadata argument:

cli <- depositsClient$new (
    service = "zenodo",
    sandbox = TRUE,
    metadata = metadata
)
print (cli)
#> <deposits client>
#>  deposits service : zenodo
#>            sandbox: TRUE
#>          url_base : https://sandbox.zenodo.org/api/
#>  Current deposits : <none>
#>
#>    hostdata : <none>
#>    metadata : 4 terms (see 'metadata' element for details)

The “metadata” component of the client now holds 4 terms (including an additional “created” datestamp). Equivalently, metadata can be added to an existing client with the deposit_fill_metadata() function:

cli <- depositsClient$new (service = "zenodo", sandbox = TRUE)
cli$deposit_fill_metadata (metadata)

Other ways of specifying and entering metadata are described in the introductory vignette. At that stage, the metadata are only associated with the local client. The following section describes how to use those metadata to initiate a deposit on an external service.

Create a new deposit

The metadata filled with the above steps can then be used to initiate a new deposit on the associated server using the deposit_new() method.

cli$deposit_new ()
#> ID of new deposit : 1065666
print (cil)
#> <deposits client>
#>  deposits service : zenodo
#>            sandbox: TRUE
#>          url_base : https://sandbox.zenodo.org/api/
#>  Current deposits : <none>
#>
#>  url_service : https://sandbox.zenodo.org/deposit/1065666
#>   deposit id : 1065666
#>     hostdata : list with 14  elements
#>     metadata : 4 terms (see 'metadata' element for details)

The client now includes several additional elements, notably a “deposit id” (stored in cli$id) giving the unique identifier for the new deposit, and a hostdata item with, in this case, 14 elements as specified by the host service. The url_service is the URL for the newly-created deposit. (Viewing in a web browser will require logging in for all private and sandbox deposits).

Uploading (and downloading) files

A deposit is really about data, not just metadata. Data can be uploaded to a deposit with the deposit_upload_file() method:

cli$deposit_upload_file (path = "<path>/<to>/my-data.dat")

Details of files associated with deposits are stored in a data.frame held as cli$hostdata$files which after running that command will include a row with an item whose “filename” will be “my-data.dat”.

cli$hostdata$files
#>                           checksum    filename filesize
#> 1 5955bb96a8fee3bc89549bde9ef9b470 my-data.dat      829
#>                                     id
#> 1 618ae9b9-af48-4b86-aa37-7b4e767dccb7
#>                                                 links.download
#> 1 https://sandbox.zenodo.org/api/files/<file-hash>/my-data.dat
#>                                                                links.self
#> 1 https://sandbox.zenodo.org/api/deposit/depositions/1065666/files/<hash>

The deposit_download_file() function does the reverse:

path <- cli$deposit_download_file ("my-data.dat")

Files are by default downloaded to the current working directory, or elsewhere specified by an additional path parameter. Unlike most methods for deposit clients, which invisibly return an updated version of the client, the deposit_download_file() returns the full local path to the downloaded file.

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.

deposits