The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
There are numerous packages that already interface with the AWS S3
protocol for object storage. Most rely directly on calls to the
low-level S3
REST API through R packages such as curl or
httr, which requires significant amounts of code to provide
high-level functionality (e.g. handling authentication, paging over
results, parsing returned XML), and is thus prone to inefficiency and
bugs. Many also implicitly assume that Amazon is the underlying
provider, making it difficult or impossible to work with a substantial
and growing number of object stores now conform to the AWS S3 standard.
These include NSF’s OpenStorageNetwork, Jetstream2
(both based on open source Redhat
CEPH), NCAR’s
Stratus (based on Western Digital S3), and MinIO Servers (another open source
implementation popular with companies and developers), as well as Google
Cloud Storage’s S3 compatibility mode.
In contrast, the MinIO Client, an open-source, AGPL-v3 software developed in the Go language by the MinIO team, provides a high-performance utility with intuitive design for working across multiple cloud-based object stores as well as local filesystems. This package provides a thin R wrapper around that client – maximizing performance and minimizing potential for maintenance and bugs. A helper utility provides a convenient way to install and update the golang binary across operating systems and architectures. The client supports parallel threads by default, intuitive handling of bucket permissions such as granting or revoking anonymous access, and persistent configurations across multiple clouds. After struggling against the limitations of many different R wrappers for S3 object stores, this is now my go-to.
You can install the development version of minioclient
from GitHub with:
# install.packages("devtools")
devtools::install_github("cboettig/minioclient")At first use, all operations will attempt to install the client
(after prompting) if not already installed. Users can also install
latest version of the minio client can be installed using
install_mc.
library(minioclient)
install_mc()The MinIO client is designed to support multiple endpoints for cloud storage, including AWS, Google Cloud Storage (via S3-compatibility), and other S3 compatible clients such as open source MinIO or Redhat CEPH storage systems. MinIO uses a syntax based around aliases to allow access across multiple platforms. Aliases can be configured using access key pairs to allow authenticated access.
By default, the client comes pre-configured with credentials for the
MinIO play platform, designed for public experimental
storage and examples. We can use mc_alias_ls() to see all
clients, specify the client we want:
mc_alias_ls("play")Some S3 object storage systems allow access without credentials.
Confusingly, attempting to access public data with invalid credentials
will still fail, so we need to specify an anonymous endpoint with no
credentials. By default, mc_alias_set will seek to use
AWS_S3_ENDPOINT, AWS_ACCESS_KEY_ID and
AWS_SECRET_ACCESS_KEY in your environment, if set. This
allows minioclient to be used in scripts with
authentication keys passed in securely as environmental variables. To
set an anonymous access, simply indicate empty credentials, like so:
mc_alias_set("anon", "s3.amazonaws.com", access_key = "", secret_key = "")Configuration of aliases is stored in a persistent configuration
file, so aliases need be created only once on a given machine. All
mc functions specify which cloud provider using a filepath
notation, <ALIAS>/<BUCKET>/<PATH>. For
instance, we can list all objects found in the bucket
gbif-open-data-us-east-1, which is a public bucket included in
the AWS Open Data Registry:
mc_ls("anon/gbif-open-data-us-east-1")
#> [1] "index.html" "occurrence/"All mc functions can also understand local filesystem
paths. Any absolute path (path starting with /), or any
relative path not recognized as a registered alias (Note: be careful not
to have local folders using the same name as remote aliases!) will be
interpreted as a local path. For instance, we can list the contents of
the local R/ directory:
mc_ls("R")
#> [1] "install_mc.R" "mc.R" "mc_alias.R" "mc_anonymous.R"
#> [5] "mc_cat.R" "mc_config_set.R" "mc_cp.R" "mc_diff.R"
#> [9] "mc_du.R" "mc_head.R" "mc_ls.R" "mc_mb.R"
#> [13] "mc_mirror.R" "mc_mv.R" "mc_rb.R" "mc_rm.R"
#> [17] "mc_sql.R" "mc_stat.R"This notation makes it easy to move data between local and remote
systems, or even between two remote systems. Let’s copy the
index.html file from GBIF to our local file system.
mc_cp("anon/gbif-open-data-us-east-1/index.html", "gbif.html")Just to prove this is indeed a local copy, we can list local directory:
fs::file_info("gbif.html")
#> # A tibble: 1 × 18
#> path type size permissions modification_time user group device_id
#> <fs::path> <fct> <fs::b> <fs::perms> <dttm> <chr> <chr> <dbl>
#> 1 gbif.html file 31.6K rw-r--r-- 2023-11-05 22:54:15 cboe… cboe… 66307
#> # ℹ 10 more variables: hard_links <dbl>, special_device_id <dbl>, inode <dbl>,
#> # block_size <dbl>, blocks <dbl>, flags <int>, generation <dbl>,
#> # access_time <dttm>, change_time <dttm>, birth_time <dttm>For any object store where we have adequate permissions, we can create new buckets:
random_name <- paste0(sample(letters, 12, replace = TRUE), collapse = "")
play_bucket <- paste0("play/play-", random_name)
mc_mb(play_bucket)
#> Bucket created successfully `play/play-hmdzuvevfzdi`.We can copy files or directories to the remote bucket:
mc_cp("anon/gbif-open-data-us-east-1/index.html", play_bucket)
mc_cp("R/", play_bucket, recursive = TRUE, verbose = TRUE)
#> `/home/cboettig/cboettig/minioclient/R/mc.R` -> `play/play-hmdzuvevfzdi/mc.R`
#> `/home/cboettig/cboettig/minioclient/R/install_mc.R` -> `play/play-hmdzuvevfzdi/install_mc.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_alias.R` -> `play/play-hmdzuvevfzdi/mc_alias.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_anonymous.R` -> `play/play-hmdzuvevfzdi/mc_anonymous.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_config_set.R` -> `play/play-hmdzuvevfzdi/mc_config_set.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_cat.R` -> `play/play-hmdzuvevfzdi/mc_cat.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_cp.R` -> `play/play-hmdzuvevfzdi/mc_cp.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_diff.R` -> `play/play-hmdzuvevfzdi/mc_diff.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_du.R` -> `play/play-hmdzuvevfzdi/mc_du.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_head.R` -> `play/play-hmdzuvevfzdi/mc_head.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_ls.R` -> `play/play-hmdzuvevfzdi/mc_ls.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_mb.R` -> `play/play-hmdzuvevfzdi/mc_mb.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_mirror.R` -> `play/play-hmdzuvevfzdi/mc_mirror.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_mv.R` -> `play/play-hmdzuvevfzdi/mc_mv.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_rb.R` -> `play/play-hmdzuvevfzdi/mc_rb.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_rm.R` -> `play/play-hmdzuvevfzdi/mc_rm.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_sql.R` -> `play/play-hmdzuvevfzdi/mc_sql.R`
#> `/home/cboettig/cboettig/minioclient/R/mc_stat.R` -> `play/play-hmdzuvevfzdi/mc_stat.R`
#> Total: 0 B, Transferred: 22.00 KiB, Speed: 314.03 KiB/sNote the use of recursive = TRUE to transfer all objects
matching the pattern. In S3 object stores, file paths are really just
prefixes, thus this query includes not only everything in the
R folder, but also README.md, since it also
matches the prefix. (Had we used the prefix R/,
README.md would not be matched and the R scripts would go
directly into play_bucket root instead of an
R/ sub-path.)
We can examine disk usage of remote objects or directories:
mc_du(play_bucket)We can also adjust permissions for anonymous access:
mc_anonymous_set(play_bucket, "download")Public objects can be accessed directly over HTTPS connection using the endpoint URL, bucket name and path:
bucket <- basename(play_bucket) # strip alias from path
# use full domain name as prefix instead:
public_url <- paste0("https://play.min.io/", bucket, "/index.html")
download.file(public_url, "index.html", quiet = TRUE)Any command supported by the minio client can be accessed using the
function mc(). This function can be used in place of any of
the above methods, or to access additional methods where no wrapper
exists, see mc("-h") for complete list. R functions such as
mc_ls() are merely helpful wrappers around the more generic
mc() utility, e.g. mc("ls play") is equivalent
to mc_ls("play"). Providing helper methods allows
tab-completion discovery of functions, R-based documentation, and
improved handling of display behavior (e.g. verbose=FALSE
by default on certain commands.) See official
mc client docs for details.
In addition to usual R documentation, users can display full help
information for any method using the argument "-h". This
includes details on optional flags and further examples.
mc_du("-h")We can now use arbitrary mc commands (see quickstart).
For example, examine file information to confirm that eTags (md5sums
here) match for these objects:
mc(paste("stat", "anon/gbif-open-data-us-east-1/index.html", paste0(play_bucket, "/index.html")))These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.