Transfer a file from iRODS to the local storage with iget() or
read an R object from an RDS file in iRODS with ireadRDS()
(see readRDS()).
Usage
iget(
logical_path,
local_path,
offset = 0,
count = 0,
verbose = FALSE,
overwrite = FALSE,
ticket = NULL
)
ireadRDS(logical_path, offset = 0, count = 0, verbose = FALSE, ticket = NULL)Arguments
- logical_path
Source path in iRODS.
- local_path
Destination path in local storage. By default, the basename of the logical path; the file will be stored in the current directory (see
getwd()).- offset
Offset in bytes into the data object. Deprecated.
- count
Maximum number of bytes to write. Deprecated.
- verbose
Whether information should be printed about the HTTP request and response.
- overwrite
Whether the local file should be overwritten if it exists. Defaults to
FALSE.- ticket
A valid iRODS ticket string. Defaults to
NULL.
Value
The R object in case of ireadRDS(), invisibly NULL in case of
iget().
The R object in case of ireadRDS(), invisibly NULL in case of iget().
See also
iput() for sending files,
isaveRDS() for sending R objects to iRODS,
saveRDS() for an R equivalent.
Transfer a file from iRODS to the local storage with iget() or
read an R object from an RDS file in iRODS with ireadRDS() (see readRDS()).
Examples
if (FALSE) { # is_irods_demo_running()
is_irods_demo_running()
DONTSHOW({
.old_config_dir <- Sys.getenv("R_USER_CONFIG_DIR")
.old_wd <- setwd(tempdir())
Sys.setenv("R_USER_CONFIG_DIR" = tempdir())
})
# connect project to server
create_irods("http://localhost:9001/irods-http-api/0.5.0", overwrite = TRUE)
# authenticate
iauth("rods", "rods")
# save the iris dataset as csv and send the file to iRODS
write.csv(iris, "iris.csv")
iput("iris.csv", "iris.csv")
# bring the file back with a different name
iget("iris.csv", "newer_iris.csv")
file.exists("newer_iris.csv") # check that it has been transferred
# send an R object to iRODS in RDS format
isaveRDS(iris, "irids_in_rds.rds")
# read it back
iris_again <- ireadRDS("irids_in_rds.rds")
iris_again
# delete objects in iRODS
irm("irids_in_rds.rds", force = TRUE)
irm("iris.csv", force = TRUE)
DONTSHOW({
setwd(.old_wd)
Sys.setenv("R_USER_CONFIG_DIR" = .old_config_dir)
})
}