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
is_irods_demo_running()
#> [1] TRUE
# \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/0.2.0", 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
#> [1] TRUE
# 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
#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#> 1 5.1 3.5 1.4 0.2 setosa
#> 2 4.9 3.0 1.4 0.2 setosa
#> 3 4.7 3.2 1.3 0.2 setosa
#> 4 4.6 3.1 1.5 0.2 setosa
#> 5 5.0 3.6 1.4 0.2 setosa
#> 6 5.4 3.9 1.7 0.4 setosa
#> 7 4.6 3.4 1.4 0.3 setosa
#> 8 5.0 3.4 1.5 0.2 setosa
#> 9 4.4 2.9 1.4 0.2 setosa
#> 10 4.9 3.1 1.5 0.1 setosa
#> 11 5.4 3.7 1.5 0.2 setosa
#> 12 4.8 3.4 1.6 0.2 setosa
#> 13 4.8 3.0 1.4 0.1 setosa
#> 14 4.3 3.0 1.1 0.1 setosa
#> 15 5.8 4.0 1.2 0.2 setosa
#> 16 5.7 4.4 1.5 0.4 setosa
#> 17 5.4 3.9 1.3 0.4 setosa
#> 18 5.1 3.5 1.4 0.3 setosa
#> 19 5.7 3.8 1.7 0.3 setosa
#> 20 5.1 3.8 1.5 0.3 setosa
#> 21 5.4 3.4 1.7 0.2 setosa
#> 22 5.1 3.7 1.5 0.4 setosa
#> 23 4.6 3.6 1.0 0.2 setosa
#> 24 5.1 3.3 1.7 0.5 setosa
#> 25 4.8 3.4 1.9 0.2 setosa
#> 26 5.0 3.0 1.6 0.2 setosa
#> 27 5.0 3.4 1.6 0.4 setosa
#> 28 5.2 3.5 1.5 0.2 setosa
#> 29 5.2 3.4 1.4 0.2 setosa
#> 30 4.7 3.2 1.6 0.2 setosa
#> 31 4.8 3.1 1.6 0.2 setosa
#> 32 5.4 3.4 1.5 0.4 setosa
#> 33 5.2 4.1 1.5 0.1 setosa
#> 34 5.5 4.2 1.4 0.2 setosa
#> 35 4.9 3.1 1.5 0.2 setosa
#> 36 5.0 3.2 1.2 0.2 setosa
#> 37 5.5 3.5 1.3 0.2 setosa
#> 38 4.9 3.6 1.4 0.1 setosa
#> 39 4.4 3.0 1.3 0.2 setosa
#> 40 5.1 3.4 1.5 0.2 setosa
#> 41 5.0 3.5 1.3 0.3 setosa
#> 42 4.5 2.3 1.3 0.3 setosa
#> 43 4.4 3.2 1.3 0.2 setosa
#> 44 5.0 3.5 1.6 0.6 setosa
#> 45 5.1 3.8 1.9 0.4 setosa
#> 46 4.8 3.0 1.4 0.3 setosa
#> 47 5.1 3.8 1.6 0.2 setosa
#> 48 4.6 3.2 1.4 0.2 setosa
#> 49 5.3 3.7 1.5 0.2 setosa
#> 50 5.0 3.3 1.4 0.2 setosa
#> 51 7.0 3.2 4.7 1.4 versicolor
#> 52 6.4 3.2 4.5 1.5 versicolor
#> 53 6.9 3.1 4.9 1.5 versicolor
#> 54 5.5 2.3 4.0 1.3 versicolor
#> 55 6.5 2.8 4.6 1.5 versicolor
#> 56 5.7 2.8 4.5 1.3 versicolor
#> 57 6.3 3.3 4.7 1.6 versicolor
#> 58 4.9 2.4 3.3 1.0 versicolor
#> 59 6.6 2.9 4.6 1.3 versicolor
#> 60 5.2 2.7 3.9 1.4 versicolor
#> 61 5.0 2.0 3.5 1.0 versicolor
#> 62 5.9 3.0 4.2 1.5 versicolor
#> 63 6.0 2.2 4.0 1.0 versicolor
#> 64 6.1 2.9 4.7 1.4 versicolor
#> 65 5.6 2.9 3.6 1.3 versicolor
#> 66 6.7 3.1 4.4 1.4 versicolor
#> 67 5.6 3.0 4.5 1.5 versicolor
#> 68 5.8 2.7 4.1 1.0 versicolor
#> 69 6.2 2.2 4.5 1.5 versicolor
#> 70 5.6 2.5 3.9 1.1 versicolor
#> 71 5.9 3.2 4.8 1.8 versicolor
#> 72 6.1 2.8 4.0 1.3 versicolor
#> 73 6.3 2.5 4.9 1.5 versicolor
#> 74 6.1 2.8 4.7 1.2 versicolor
#> 75 6.4 2.9 4.3 1.3 versicolor
#> 76 6.6 3.0 4.4 1.4 versicolor
#> 77 6.8 2.8 4.8 1.4 versicolor
#> 78 6.7 3.0 5.0 1.7 versicolor
#> 79 6.0 2.9 4.5 1.5 versicolor
#> 80 5.7 2.6 3.5 1.0 versicolor
#> 81 5.5 2.4 3.8 1.1 versicolor
#> 82 5.5 2.4 3.7 1.0 versicolor
#> 83 5.8 2.7 3.9 1.2 versicolor
#> 84 6.0 2.7 5.1 1.6 versicolor
#> 85 5.4 3.0 4.5 1.5 versicolor
#> 86 6.0 3.4 4.5 1.6 versicolor
#> 87 6.7 3.1 4.7 1.5 versicolor
#> 88 6.3 2.3 4.4 1.3 versicolor
#> 89 5.6 3.0 4.1 1.3 versicolor
#> 90 5.5 2.5 4.0 1.3 versicolor
#> 91 5.5 2.6 4.4 1.2 versicolor
#> 92 6.1 3.0 4.6 1.4 versicolor
#> 93 5.8 2.6 4.0 1.2 versicolor
#> 94 5.0 2.3 3.3 1.0 versicolor
#> 95 5.6 2.7 4.2 1.3 versicolor
#> 96 5.7 3.0 4.2 1.2 versicolor
#> 97 5.7 2.9 4.2 1.3 versicolor
#> 98 6.2 2.9 4.3 1.3 versicolor
#> 99 5.1 2.5 3.0 1.1 versicolor
#> 100 5.7 2.8 4.1 1.3 versicolor
#> 101 6.3 3.3 6.0 2.5 virginica
#> 102 5.8 2.7 5.1 1.9 virginica
#> 103 7.1 3.0 5.9 2.1 virginica
#> 104 6.3 2.9 5.6 1.8 virginica
#> 105 6.5 3.0 5.8 2.2 virginica
#> 106 7.6 3.0 6.6 2.1 virginica
#> 107 4.9 2.5 4.5 1.7 virginica
#> 108 7.3 2.9 6.3 1.8 virginica
#> 109 6.7 2.5 5.8 1.8 virginica
#> 110 7.2 3.6 6.1 2.5 virginica
#> 111 6.5 3.2 5.1 2.0 virginica
#> 112 6.4 2.7 5.3 1.9 virginica
#> 113 6.8 3.0 5.5 2.1 virginica
#> 114 5.7 2.5 5.0 2.0 virginica
#> 115 5.8 2.8 5.1 2.4 virginica
#> 116 6.4 3.2 5.3 2.3 virginica
#> 117 6.5 3.0 5.5 1.8 virginica
#> 118 7.7 3.8 6.7 2.2 virginica
#> 119 7.7 2.6 6.9 2.3 virginica
#> 120 6.0 2.2 5.0 1.5 virginica
#> 121 6.9 3.2 5.7 2.3 virginica
#> 122 5.6 2.8 4.9 2.0 virginica
#> 123 7.7 2.8 6.7 2.0 virginica
#> 124 6.3 2.7 4.9 1.8 virginica
#> 125 6.7 3.3 5.7 2.1 virginica
#> 126 7.2 3.2 6.0 1.8 virginica
#> 127 6.2 2.8 4.8 1.8 virginica
#> 128 6.1 3.0 4.9 1.8 virginica
#> 129 6.4 2.8 5.6 2.1 virginica
#> 130 7.2 3.0 5.8 1.6 virginica
#> 131 7.4 2.8 6.1 1.9 virginica
#> 132 7.9 3.8 6.4 2.0 virginica
#> 133 6.4 2.8 5.6 2.2 virginica
#> 134 6.3 2.8 5.1 1.5 virginica
#> 135 6.1 2.6 5.6 1.4 virginica
#> 136 7.7 3.0 6.1 2.3 virginica
#> 137 6.3 3.4 5.6 2.4 virginica
#> 138 6.4 3.1 5.5 1.8 virginica
#> 139 6.0 3.0 4.8 1.8 virginica
#> 140 6.9 3.1 5.4 2.1 virginica
#> 141 6.7 3.1 5.6 2.4 virginica
#> 142 6.9 3.1 5.1 2.3 virginica
#> 143 5.8 2.7 5.1 1.9 virginica
#> 144 6.8 3.2 5.9 2.3 virginica
#> 145 6.7 3.3 5.7 2.5 virginica
#> 146 6.7 3.0 5.2 2.3 virginica
#> 147 6.3 2.5 5.0 1.9 virginica
#> 148 6.5 3.0 5.2 2.0 virginica
#> 149 6.2 3.4 5.4 2.3 virginica
#> 150 5.9 3.0 5.1 1.8 virginica
# 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)
# }