osf_upload: Upload files to OSF

In ropensci/osfr: Interface to the 'Open Science Framework' ('OSF')

Upload files to OSF

Description

Upload local files to a project, component, or directory on OSF.

Usage

osf_upload(
  x,
  path,
  recurse = FALSE,
  conflicts = "error",
  progress = FALSE,
  verbose = FALSE
)

Arguments

x	The upload destination on OSF. Can be one of the following: An osf_tbl_node with a single project or component. An osf_tbl_file with a single directory.
path	A character vector of paths pointing to existing local files and/directories.
recurse	If TRUE, fully recurse directories included in path. You can also control the number of levels to recurse by specifying a positive number.
conflicts	This determines what happens when a file with the same name exists at the specified destination. Can be one of the following: "error" (the default): throw an error and abort the file transfer operation. "skip": skip the conflicting file(s) and continue transferring the remaining files. "overwrite": replace the existing file with the transferred copy.
progress	Logical, if TRUE progress bars are displayed for each file transfer. Mainly useful for transferring large files. For tracking lots of small files, setting verbose = TRUE is more informative.
verbose	Logical, indicating whether to print informative messages about interactions with the OSF API (default FALSE).

Value

An osf_tbl_file containing the uploaded files and directories that were directly specified in path.

File and directory paths

The x argument indicates where on OSF the files will be uploaded (i.e., the destination). The path argument indicates what will be uploaded, which can include a combination of files and directories.

When path points to a local file, the file is uploaded to the root of the specified OSF destination, regardless of where it's on your local machine (i.e., the intermediate paths are not preserved). For example, the following would would upload both a.txt and b.txt to the root of my_proj:

osf_upload(my_proj, c("a.txt", "subdir/b.txt"))`

When path points to a local directory, a corresponding directory will be created at the root of the OSF destination, x, and any files within the local directory are uploaded to the new OSF directory. Therefore, we could maintain the directory structure in the above example by passing b.txt's parent directory to path instead of the file itself:

osf_upload(my_proj, c("a.txt", "subdir2"))

Likewise, osf_upload(my_proj, path = ".") will upload your entire current working directory to the specified OSF destination.

Uploading to subdirectories

In order to upload directly to an existing OSF directory you would first need to retrieve the directory as an osf_tbl_file. This can be accomplished by passing the directory's unique identifier to osf_retrieve_file(), or, if you don't have the ID handy, you can use osf_ls_files() to retrieve the directory by name.

# search for the 'rawdata' subdirectory within top-level 'data' directory
target_dir <- osf_ls_files(my_proj, path = "data", pattern = "rawdata")
# upload 'a.txt' to data/rawdata/ on OSF
osf_upload(target_dir, path = "a.txt")

A note about synchronization

While osf_download() and osf_upload() allow you to conveniently shuttle files back and forth between OSF and your local machine, it's important to note that they are not file synchronization functions. In contrast to something like rsync, osf_download()/osf_upload() do not take into account a file's contents or modification time. Whether you're uploading or downloading, if conflicts = "overwrite", osfr will overwrite the existing file regardless of whether it is the more recent copy. You have been warned.

See Also

• osf_download() for downloading files and directories from OSF.

• osf_ls_files() for listing files and directories on OSF.

Examples

## Not run: 
# Create an example file to upload to our example project
write.csv(iris, file = "iris.csv")
project <- osf_create_project("Flower Data")

# Upload the first version
osf_upload(project,"iris.csv")

# Modify the data file, upload version 2, and view it on OSF
write.csv(subset(iris, Species != "setosa"), file = "iris.csv")
project %>%
  osf_upload("iris.csv", conflicts = "overwrite") %>%
  osf_open()

## End(Not run)

ropensci/osfr documentation built on Sept. 29, 2022, 2:14 a.m.