Get data from a Zenodo record

get_from_zenodo() allows you to easy download a Zenodo record or a Zenodo file.

This function only works for Zenodo created DOIs (not when the DOI is, for example, derived from Zookeys).

get_from_zenodo(doi, path = ".", file = NULL, parallel = FALSE)

Arguments

doi: A string indicating a Zenodo DOI (Digital Object Identifier) starting with "10.5281/zenodo.". See the Examples section to learn more.
path: (optional) a string indicating a directory path where the data must be downloaded (default: ".").
file: (optional) a character object with the names of the files that must be downloaded. If NULL, the function will download the entire record (default: NULL).
parallel: (optional) a logical value indicating if the function must run a number of parallel processes, each downloading another file (requires the parallel package). This is useful when multiple large files are present in the Zenodo record, which otherwise would be downloaded sequentially. Of course, the operation is limited by bandwidth and traffic limitations (default: FALSE).

Value

A character object with the paths for all the files downloaded.

Details

Requirements

This function requires an internet connection and the curl, jsonlite, parallel, and tools packages to work.

If you don't have any or one of the packages mentioned above, you can install them with install.packages("curl", "jsonlite", "parallel", "tools").

Zenodo API

You can find more about the Zenodo API at https://developers.zenodo.org/.

License

get_from_zenodo() code is based on the download_zenodo() function found in the inborutils package of the Research Institute for Nature and Forest (INBO). download_zenodo() was created by Hans Van Calster (hans.vancalster@inbo.be) and Floris Vanderhaeghe (floris.vanderhaeghe@inbo.be).

We give our thanks for the INBO institute and for all developers involved in this piece of software.

Please note that this code comes with an MIT License. You can read the latter below.

Copyright (c) 2016 Instituut voor Natuur en Bosonderzoek (INBO)

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

Examples

if (FALSE) {
## Downloading a single file from a Zenodo record

path <- tempdir()
file <- "sleep-diary.txt"

get_from_zenodo(
    doi = "10.5281/zenodo.4898822", path = path, file = file
    )

readLines(file.path(path, file))

## Downloading all the files from a Zenodo record

get_from_zenodo(
    doi = "10.5281/zenodo.4898822", path = tempdir(), file = NULL
    )

## Downloading all the files from a Zenodo record using parallel
## computation

get_from_zenodo(
    doi = "10.5281/zenodo.4898822", path = tempdir(), file = NULL,
    parallel = TRUE
    )
}