Using docker with stevedore

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Rich FitzJohn

2020-01-12

stevedore is an R package for interacting with docker from R. With stevedore you can

Almost everything that can be done with the docker command line client (the main exception being that is not possible to send input to a container as if you were on a terminal).

stevedore directly interacts with the docker server over its HTTP API. This gives a more direct access to docker than going via the command line.

This vignette quickly walks through the core features of the package. Because stevedore wraps the docker API directly there are many more arguments that can be used than are covered here. But this covers the core use.

The main function in the package is docker_client; this will construct an object with which we can talk with the docker server. By default this will look at a number of environment variables and try to connect to the correct daemon. See ?docker_client for information on controlling creating the connection.

The client object looks a lot like an R6 object (though it is implemented differently because the interface here is automatically generated in ways that don’t play nicely with R6). But if you are at all familiar with R6 objects it should seem quite familiar.

In addition there are “collection” objects (e.g., container) that are accessed using $, like a directory structure

The interface is designed similarly to the command line docker client (and to the Python docker client), where container commands are within the container collection and image commands are within the image collection and so on (the main difference with the command line client is that the container commands are not at the top level, so it is docker$container$run(...) not docker$run(...)).

To run a container, the docker$container$run command follows the semantics of the command line client and will

This is a docker_stream object and codes the output stream using the stream attribute (it can otherwise be treated as a character vector).

The “container” element is an object that can be used to interact with a container

For example the function path_stat gets some information about paths on the container:

which is another object with methods that can be invoked to find out about the image, e.g.:

Containers

The $container object includes methods for interacting with containers:

docker$container

## <docker_container_collection>
##   create(image, cmd = NULL, hostname = NULL, domainname = NULL,
##       user = NULL, attach_stdin = NULL, attach_stdout = NULL,
##       attach_stderr = NULL, ports = NULL, tty = NULL,
##       open_stdin = NULL, stdin_once = NULL, env = NULL,
##       health_check = NULL, args_escaped = NULL, volumes = NULL,
##       working_dir = NULL, entrypoint = NULL, network_disabled = NULL,
##       mac_address = NULL, on_build = NULL, labels = NULL,
##       stop_signal = NULL, stop_timeout = NULL, shell = NULL,
##       host_config = NULL, network = NULL, name = NULL)
##   get(id)
##   help(help_type = getOption("help_type"))
##   list(all = NULL, limit = NULL, size = NULL, filters = NULL)
##   prune(filters = NULL)
##   remove(id, delete_volumes = NULL, force = NULL, link = NULL)
##   run(image, cmd = NULL, ..., detach = FALSE, rm = FALSE,
##       stream = stdout(), host_config = NULL)

$create creates a new container (similar to docker container create on the command line) but does not start it.

x <- docker$container$create("hello-world", name = "hello-stevedore")
x

## <docker_container>
##   commit(repo = NULL, tag = NULL, author = NULL, changes = NULL,
##       comment = NULL, pause = NULL, hostname = NULL, domainname = NULL,
##       user = NULL, attach_stdin = NULL, attach_stdout = NULL,
##       attach_stderr = NULL, exposed_ports = NULL, tty = NULL,
##       open_stdin = NULL, stdin_once = NULL, env = NULL, cmd = NULL,
##       healthcheck = NULL, args_escaped = NULL, image = NULL,
##       volumes = NULL, working_dir = NULL, entrypoint = NULL,
##       network_disabled = NULL, mac_address = NULL, on_build = NULL,
##       labels = NULL, stop_signal = NULL, stop_timeout = NULL,
##       shell = NULL)
##   cp_in(src, dest)
##   cp_out(src, dest)
##   diff()
##   exec(cmd, stdin = NULL, stdout = TRUE, stderr = TRUE,
##       detach_keys = NULL, tty = NULL, env = NULL, privileged = NULL,
##       user = NULL, working_dir = NULL, detach = FALSE,
##       stream = stdout())
##   exec_create(cmd, stdin = NULL, stdout = TRUE, stderr = TRUE,
##       detach_keys = NULL, tty = NULL, env = NULL, privileged = NULL,
##       user = NULL, working_dir = NULL)
##   export()
##   get_archive(path, dest)
##   help(help_type = getOption("help_type"))
##   id()
##   image()
##   inspect(reload = TRUE)
##   kill(signal = NULL)
##   labels(reload = TRUE)
##   logs(follow = NULL, stdout = TRUE, stderr = TRUE, since = NULL,
##       until = NULL, timestamps = NULL, tail = NULL, stream = stdout())
##   name()
##   path_stat(path)
##   pause()
##   ports(reload = TRUE)
##   put_archive(src, path, no_overwrite_dir_non_dir = NULL)
##   reload()
##   remove(delete_volumes = NULL, force = NULL, link = NULL)
##   rename(name)
##   resize(h = NULL, w = NULL)
##   restart(t = NULL)
##   start(detach_keys = NULL)
##   stats()
##   status(reload = TRUE)
##   stop(t = NULL)
##   top(ps_args = NULL)
##   unpause()
##   update(cpu_shares = NULL, memory = NULL, cgroup_parent = NULL,
##       blkio_weight = NULL, blkio_weight_device = NULL,
##       blkio_device_read_bps = NULL, blkio_device_write_bps = NULL,
##       blkio_device_read_iops = NULL, blkio_device_write_iops = NULL,
##       cpu_period = NULL, cpu_quota = NULL, cpu_realtime_period = NULL,
##       cpu_realtime_runtime = NULL, cpuset_cpus = NULL,
##       cpuset_mems = NULL, devices = NULL, device_cgroup_rules = NULL,
##       disk_quota = NULL, kernel_memory = NULL,
##       memory_reservation = NULL, memory_swap = NULL,
##       memory_swappiness = NULL, nano_cpus = NULL,
##       oom_kill_disable = NULL, init = NULL, pids_limit = NULL,
##       ulimits = NULL, cpu_count = NULL, cpu_percent = NULL,
##       io_maximum_iops = NULL, io_maximum_bandwidth = NULL,
##       restart_policy = NULL)
##   wait(condition = NULL)

$get creates a docker_container object from an container id or name:

y <- docker$container$get("hello-stevedore")
x$id()

## [1] "25ba2590b21fac453aec605af5af7f1595d2169e1324254d97f5a08701b59e6c"

y$id()

## [1] "25ba2590b21fac453aec605af5af7f1595d2169e1324254d97f5a08701b59e6c"

$list() lists containers (like docker list on the command line) - by default showing only running containers

docker$container$list()

##  [1] id               names            image            image_id
##  [5] command          created          ports            size_rw
##  [9] size_root_fs     labels           state            status
## [13] host_config      network_settings mounts           name
## <0 rows> (or 0-length row.names)

docker$container$list(all = TRUE, limit = 2)

##                                                                 id
## 1 25ba2590b21fac453aec605af5af7f1595d2169e1324254d97f5a08701b59e6c
## 2 e414940048abbea2a66c33fb5191cc881764955ae0b9110ab48ce29cc29ddcce
##          names
## 1 hello-st....
## 2 frosty_b....
##                                                                     image
## 1                                                             hello-world
## 2 sha256:fce289e99eb9bca977dae136fbe2a82b6b7d4c372474c9235adc1741675f587e
##                                                                  image_id
## 1 sha256:fce289e99eb9bca977dae136fbe2a82b6b7d4c372474c9235adc1741675f587e
## 2 sha256:fce289e99eb9bca977dae136fbe2a82b6b7d4c372474c9235adc1741675f587e
##   command    created        ports size_rw size_root_fs labels   state
## 1  /hello 1578823525 characte....      NA           NA        created
## 2  /hello 1578823523 characte....      NA           NA         exited
##                    status host_config network_settings       mounts
## 1                 Created     default     list(bri.... characte....
## 2 Exited (0) 1 second ago     default     list(bri.... characte....
##              name
## 1 hello-stevedore
## 2   frosty_banzai

$remove() removes a container by name or id:

docker$container$remove("hello-stevedore")

## NULL

$prune() removes non-running containers (i.e., containers that have exited or containers that have been created but not yet started)

docker$container$prune()

## $containers_deleted
## [1] "e414940048abbea2a66c33fb5191cc881764955ae0b9110ab48ce29cc29ddcce"
##
## $space_reclaimed
## [1] 0

Working with containers

After creating a container object, there are many more methods to use - all apply to the individual container

x <- docker$container$create("richfitz/iterate", c("1000", "1"))

Most are analogues of similarly named docker command line functions.

First, there are some basic query methods - $id(), $name() and $labels()

x$id()

## [1] "b553018482d2e4119e20c9ccc54fd7a14e6aa7843f630a5266548f31d755211d"

x$name()

## [1] "angry_snyder"

x$labels()

## stevedore_version
##           "0.0.1"

More detailed information (much more detailed) can be retrieved with the $inspect() method

x$inspect()

## $id
## [1] "b553018482d2e4119e20c9ccc54fd7a14e6aa7843f630a5266548f31d755211d"
##
## $created
## [1] "2020-01-12T10:05:25.3062459Z"
##
## $path
## [1] "/usr/local/bin/iterate"
##
## $args
## [1] "1000" "1"
##
## $state
## $state$status
## [1] "created"
##
## $state$running
## [1] FALSE
##
## $state$paused
## [1] FALSE
##
## $state$restarting
## [1] FALSE
##
## $state$oom_killed
## [1] FALSE
##
## $state$dead
## [1] FALSE
##
## $state$pid
## [1] 0
##
## $state$exit_code
## [1] 0
##
## $state$error
## [1] ""
##
## $state$started_at
## [1] "0001-01-01T00:00:00Z"
##
## $state$finished_at
## [1] "0001-01-01T00:00:00Z"
##
##
## $image
## [1] "sha256:56b0d98ceb5a402ea61c63ab94a8e7f305cde36e3aa8f080a0b7ab1a8a659e7c"
##
## $resolv_conf_path
## [1] ""
##
## $hostname_path
## [1] ""
##
## $hosts_path
## [1] ""
##
## $log_path
## [1] ""
##
## $node
## NULL
##
## $name
## [1] "/angry_snyder"
##
## $restart_count
## [1] 0
##
## $driver
## [1] "overlay2"
##
## $mount_label
## [1] ""
##
## $process_label
## [1] ""
##
## $app_armor_profile
## [1] ""
##
## $exec_ids
## character(0)
##
## $host_config
## $host_config$cpu_shares
## [1] 0
##
## $host_config$memory
## [1] 0
##
## $host_config$cgroup_parent
## [1] ""
##
## $host_config$blkio_weight
## [1] 0
##
## $host_config$blkio_weight_device
## [1] path   weight
## <0 rows> (or 0-length row.names)
##
## $host_config$blkio_device_read_bps
## [1] path rate
## <0 rows> (or 0-length row.names)
##
## $host_config$blkio_device_write_bps
## [1] path rate
## <0 rows> (or 0-length row.names)
##
## $host_config$blkio_device_read_iops
## [1] path rate
## <0 rows> (or 0-length row.names)
##
## $host_config$blkio_device_write_iops
## [1] path rate
## <0 rows> (or 0-length row.names)
##
## $host_config$cpu_period
## [1] 0
##
## $host_config$cpu_quota
## [1] 0
##
## $host_config$cpu_realtime_period
## [1] 0
##
## $host_config$cpu_realtime_runtime
## [1] 0
##
## $host_config$cpuset_cpus
## [1] ""
##
## $host_config$cpuset_mems
## [1] ""
##
## $host_config$devices
## [1] path_on_host       path_in_container  cgroup_permissions
## <0 rows> (or 0-length row.names)
##
## $host_config$device_cgroup_rules
## character(0)
##
## $host_config$disk_quota
## [1] 0
##
## $host_config$kernel_memory
## [1] 0
##
## $host_config$memory_reservation
## [1] 0
##
## $host_config$memory_swap
## [1] 0
##
## $host_config$memory_swappiness
## [1] NA
##
## $host_config$nano_cpus
## [1] NA
##
## $host_config$oom_kill_disable
## [1] FALSE
##
## $host_config$init
## [1] NA
##
## $host_config$pids_limit
## [1] 0
##
## $host_config$ulimits
## [1] name soft hard
## <0 rows> (or 0-length row.names)
##
## $host_config$cpu_count
## [1] 0
##
## $host_config$cpu_percent
## [1] 0
##
## $host_config$io_maximum_iops
## [1] 0
##
## $host_config$io_maximum_bandwidth
## [1] 0
##
## $host_config$binds
## character(0)
##
## $host_config$container_idfile
## [1] ""
##
## $host_config$log_config
## $host_config$log_config$type
## [1] "json-file"
##
## $host_config$log_config$config
## character(0)
##
##
## $host_config$network_mode
## [1] "default"
##
## $host_config$port_bindings
## NULL
##
## $host_config$restart_policy
## $host_config$restart_policy$name
## [1] ""
##
## $host_config$restart_policy$maximum_retry_count
## [1] 0
##
##
## $host_config$auto_remove
## [1] FALSE
##
## $host_config$volume_driver
## [1] ""
##
## $host_config$volumes_from
## character(0)
##
## $host_config$mounts
## [1] target         source         type           read_only
## [5] consistency    bind_options   volume_options tmpfs_options
## <0 rows> (or 0-length row.names)
##
## $host_config$cap_add
## character(0)
##
## $host_config$cap_drop
## character(0)
##
## $host_config$dns
## character(0)
##
## $host_config$dns_options
## character(0)
##
## $host_config$dns_search
## character(0)
##
## $host_config$extra_hosts
## character(0)
##
## $host_config$group_add
## character(0)
##
## $host_config$ipc_mode
## [1] "shareable"
##
## $host_config$cgroup
## [1] ""
##
## $host_config$links
## character(0)
##
## $host_config$oom_score_adj
## [1] 0
##
## $host_config$pid_mode
## [1] ""
##
## $host_config$privileged
## [1] FALSE
##
## $host_config$publish_all_ports
## [1] FALSE
##
## $host_config$readonly_rootfs
## [1] FALSE
##
## $host_config$security_opt
## character(0)
##
## $host_config$storage_opt
## NULL
##
## $host_config$tmpfs
## NULL
##
## $host_config$uts_mode
## [1] ""
##
## $host_config$userns_mode
## [1] ""
##
## $host_config$shm_size
## [1] 67108864
##
## $host_config$sysctls
## NULL
##
## $host_config$runtime
## [1] NA
##
## $host_config$console_size
## [1] 0 0
##
## $host_config$isolation
## [1] ""
##
## $host_config$masked_paths
##  [1] "/proc/asound"        "/proc/acpi"          "/proc/kcore"
##  [4] "/proc/keys"          "/proc/latency_stats" "/proc/timer_list"
##  [7] "/proc/timer_stats"   "/proc/sched_debug"   "/proc/scsi"
## [10] "/sys/firmware"
##
## $host_config$readonly_paths
## [1] "/proc/bus"           "/proc/fs"            "/proc/irq"
## [4] "/proc/sys"           "/proc/sysrq-trigger"
##
##
## $graph_driver
## $graph_driver$name
## [1] "overlay2"
##
## $graph_driver$data
##                                                                                                                                                                                                                                                                                           lower_dir
## "/var/lib/docker/overlay2/2ac2803a954a813a808e9c1d1f63edf0153ef0dbc109d1c12db372dc2c1104d7-init/diff:/var/lib/docker/overlay2/530d1f73dec177ad03a0ee31ad04d0802bf29925cd2eed2b8e5f49258c6824a3/diff:/var/lib/docker/overlay2/e1a21604d525ede2c5e9e6d59ac7dceb33bc7469ad98cc9997477a38c310305c/diff"
##                                                                                                                                                                                                                                                                                          merged_dir
##                                                                                                                                                                                                  "/var/lib/docker/overlay2/2ac2803a954a813a808e9c1d1f63edf0153ef0dbc109d1c12db372dc2c1104d7/merged"
##                                                                                                                                                                                                                                                                                           upper_dir
##                                                                                                                                                                                                    "/var/lib/docker/overlay2/2ac2803a954a813a808e9c1d1f63edf0153ef0dbc109d1c12db372dc2c1104d7/diff"
##                                                                                                                                                                                                                                                                                            work_dir
##                                                                                                                                                                                                    "/var/lib/docker/overlay2/2ac2803a954a813a808e9c1d1f63edf0153ef0dbc109d1c12db372dc2c1104d7/work"
##
##
## $size_rw
## [1] NA
##
## $size_root_fs
## [1] NA
##
## $mounts
## [1] type        name        source      destination driver      mode
## [7] rw          propagation
## <0 rows> (or 0-length row.names)
##
## $config
## $config$hostname
## [1] "b553018482d2"
##
## $config$domainname
## [1] ""
##
## $config$user
## [1] ""
##
## $config$attach_stdin
## [1] FALSE
##
## $config$attach_stdout
## [1] FALSE
##
## $config$attach_stderr
## [1] FALSE
##
## $config$exposed_ports
## NULL
##
## $config$tty
## [1] FALSE
##
## $config$open_stdin
## [1] FALSE
##
## $config$stdin_once
## [1] FALSE
##
## $config$env
## [1] "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
##
## $config$cmd
## [1] "1000" "1"
##
## $config$healthcheck
## NULL
##
## $config$args_escaped
## [1] NA
##
## $config$image
## [1] "richfitz/iterate"
##
## $config$volumes
## NULL
##
## $config$working_dir
## [1] ""
##
## $config$entrypoint
## [1] "/usr/local/bin/iterate"
##
## $config$network_disabled
## [1] NA
##
## $config$mac_address
## [1] NA
##
## $config$on_build
## character(0)
##
## $config$labels
## stevedore_version
##           "0.0.1"
##
## $config$stop_signal
## [1] NA
##
## $config$stop_timeout
## [1] NA
##
## $config$shell
## character(0)
##
##
## $network_settings
## $network_settings$bridge
## [1] ""
##
## $network_settings$sandbox_id
## [1] ""
##
## $network_settings$hairpin_mode
## [1] FALSE
##
## $network_settings$link_local_ipv6_address
## [1] ""
##
## $network_settings$link_local_ipv6_prefix_len
## [1] 0
##
## $network_settings$ports
## list()
##
## $network_settings$sandbox_key
## [1] ""
##
## $network_settings$secondary_ipaddresses
## [1] addr       prefix_len
## <0 rows> (or 0-length row.names)
##
## $network_settings$secondary_ipv6_addresses
## [1] addr       prefix_len
## <0 rows> (or 0-length row.names)
##
## $network_settings$endpoint_id
## [1] ""
##
## $network_settings$gateway
## [1] ""
##
## $network_settings$global_ipv6_address
## [1] ""
##
## $network_settings$global_ipv6_prefix_len
## [1] 0
##
## $network_settings$ip_address
## [1] ""
##
## $network_settings$ip_prefix_len
## [1] 0
##
## $network_settings$ipv6_gateway
## [1] ""
##
## $network_settings$mac_address
## [1] ""
##
## $network_settings$networks
## $network_settings$networks$bridge
## $network_settings$networks$bridge$ipam_config
## NULL
##
## $network_settings$networks$bridge$links
## character(0)
##
## $network_settings$networks$bridge$aliases
## character(0)
##
## $network_settings$networks$bridge$network_id
## [1] ""
##
## $network_settings$networks$bridge$endpoint_id
## [1] ""
##
## $network_settings$networks$bridge$gateway
## [1] ""
##
## $network_settings$networks$bridge$ip_address
## [1] ""
##
## $network_settings$networks$bridge$ip_prefix_len
## [1] 0
##
## $network_settings$networks$bridge$ipv6_gateway
## [1] ""
##
## $network_settings$networks$bridge$global_ipv6_address
## [1] ""
##
## $network_settings$networks$bridge$global_ipv6_prefix_len
## [1] 0
##
## $network_settings$networks$bridge$mac_address
## [1] ""
##
## $network_settings$networks$bridge$driver_opts
## NULL

The image used by a container can be retrieved with the $image() method

x$image()

## <docker_image>
##   export()
##   help(help_type = getOption("help_type"))
##   history()
##   id()
##   inspect(reload = TRUE)
##   labels(reload = TRUE)
##   name()
##   reload()
##   remove(force = NULL, noprune = NULL)
##   short_id()
##   tag(repo, tag = NULL)
##   tags(reload = TRUE)
##   untag(repo_tag)

(see below for working with images).

The status of the container (created, running, exited, paused, etc) can be read with $status()

x$status()

## [1] "created"

The container created by by $create is not running - the $start() method will start it:

x$start()
x$status()

## [1] "running"

Once the container is running we can query to see what processes are running in it with $top (standing for Table Of Processes)

x$top()

##    PID USER TIME                                         COMMAND
## 1 2918 root 0:00 {iterate} /bin/sh /usr/local/bin/iterate 1000 1
## 2 2953 root 0:00                                         sleep 1

We can also get the logs:

x$logs()

## O> Doing 1000 iterations with interval 1
## O> Iteration 1...

This returns a special object type docker_stream which allows control over formatting with format() - the style argument controls how stderr and stdout are printed. There is a stream attribute that can be used to separate out lines too. If a tty was allocated with tty = TRUE the output will be a plain character vector

format(x$logs(), style = "plain")

## [1] "Doing 1000 iterations with interval 1\n"
## [2] "Iteration 1...\n"

It can generally be treated as a character vector:

x$logs()[1:2]

## [1] "Doing 1000 iterations with interval 1\n"
## [2] "Iteration 1...\n"

The $logs() method can be used to do a blocking wait on a container. Pass follow = TRUE to follow the logs. You will want to provide a stream argument too, which is where to stream the log to. This can be stdout() or stderr(), a file or an R connection.

y <- docker$container$create("richfitz/iterate", c("10", "0.1"))
y$start()
y$logs(stream = stdout(), follow = TRUE)

## O> Doing 10 iterations with interval 0.1
## O> Iteration 1...
## O> Iteration 2...
## O> Iteration 3...
## O> Iteration 4...
## O> Iteration 5...
## O> Iteration 6...
## O> Iteration 7...
## O> Iteration 8...
## O> Iteration 9...
## O> Iteration 10...
## O> Done!

If running this interactively, the logs will print one line at a time - once control returns to R the container has exited. You can escape this streaming using whatever method you use to interrupt an R calculation (depends on which GUI/IDE you are using) but the container will continue regardless - we are just observing a running container.

y$status()

## [1] "exited"

The other way of blocking until a container has finished is with $wait() which blocks until the container exits, then returns the exit code.

y$start()
y$wait()

## $exit_code
## [1] 0

Calling $wait() on an exited container is fine, and will just return immediately:

y$wait()

## $exit_code
## [1] 0

Containers can be paused with $pause()

x$pause()

## NULL

x$status()

## [1] "paused"

Once paused, they can be restarted with $unpause()

x$unpause()

## NULL

x$status()

## [1] "running"

Additionally, containers can be restarted with $restart()

x$restart(t = 0)

## NULL

x$logs(tail = 5)

## O> Iteration 4...
## O> Iteration 5...
## O> Iteration 6...
## O> Doing 1000 iterations with interval 1
## O> Iteration 1...

Containers can be stopped with $stop() and removed with $remove() (calling $remove(force = TRUE) will kill the container before removing.

x$stop(t = 0)

## NULL

x$remove()

## NULL

Once a container has been removed most methods will not work properly:

x$status()

## Error: No such container: b553018482d2e4119e20c9ccc54fd7a14e6aa7843f630a5266548f31d755211d

Information about ports (for containers that expose them) can be retrieved with $ports(). The nginx image creates a web server/proxy that exposes port 80 from the container. We can map that to a random port by asking docker to expose port 80 but not saying what to map it to:

nginx <- docker$container$run("nginx", ports = 80,
                              detach = TRUE, rm = TRUE,
                              name = "stevedore-nginx")
nginx$ports()

##   container_port protocol host_ip host_port
## 1             80      tcp 0.0.0.0     32768

(alternatively, use ports = TRUE to act like docker run’s -P and "publish all ports to random ports).

This shows that the port exposed by the the container (80) is mapped to the port 32768 on the host. We can use this to communicate with the server:

url <- sprintf("http://localhost:%s", nginx$ports()$host_port)
curl::parse_headers(curl::curl_fetch_memory(url)$headers)

## [1] "HTTP/1.1 200 OK"
## [2] "Server: nginx/1.17.7"
## [3] "Date: Sun, 12 Jan 2020 10:05:34 GMT"
## [4] "Content-Type: text/html"
## [5] "Content-Length: 612"
## [6] "Last-Modified: Tue, 24 Dec 2019 13:07:53 GMT"
## [7] "Connection: keep-alive"
## [8] "ETag: \"5e020da9-264\""
## [9] "Accept-Ranges: bytes"

nginx$stop(t = 0)

## NULL

Run commands in running containers with `exec`

With the command-line tool, docker exec <container name> <command> lets you run an arbitrary command within a running container. stevedore does this with the exec method of a container object.

Reasons for doing this include debugging (using arbitrary commands to inspect/interact with a container while it does its primary task) but it can also be used in deployment (e.g., sending a “go” signal after copying files into the container).

To demonstrate, we need a long running container:

x <- docker$container$run("richfitz/iterate", c("1000", "10"),
                          detach = TRUE, rm = TRUE)
x$status()

## [1] "running"

With the container running we can run additional commands:

res <- x$exec("ls")

## O> bin
## O> dev
## O> etc
## O> home
## O> lib
## O> media
## O> mnt
## O> opt
## O> proc
## O> root
## O> run
## O> sbin
## O> srv
## O> sys
## O> tmp
## O> usr
## O> var

This streams the output of the command by default (to the connection indicated by the stream) argument. Output is also returned as part of the object:

res

## $id
## [1] "62e5e653b88bda606b07b286bd27ca8d0b653e3000e76004463b609974722d0e"
##
## $exit_code
## [1] 0
##
## $details
## $details$can_remove
## [1] FALSE
##
## $details$detach_keys
## [1] ""
##
## $details$id
## [1] "62e5e653b88bda606b07b286bd27ca8d0b653e3000e76004463b609974722d0e"
##
## $details$running
## [1] FALSE
##
## $details$exit_code
## [1] 0
##
## $details$process_config
## $details$process_config$privileged
## [1] FALSE
##
## $details$process_config$user
## [1] NA
##
## $details$process_config$tty
## [1] FALSE
##
## $details$process_config$entrypoint
## [1] "ls"
##
## $details$process_config$arguments
## character(0)
##
##
## $details$open_stdin
## [1] FALSE
##
## $details$open_stderr
## [1] TRUE
##
## $details$open_stdout
## [1] TRUE
##
## $details$container_id
## [1] "9317cd764a3c2648de3d284ea084466afc1512fba48625233498ee1dc9754da2"
##
## $details$pid
## [1] 3673
##
##
## $output
## O> bin
## O> dev
## O> etc
## O> home
## O> lib
## O> media
## O> mnt
## O> opt
## O> proc
## O> root
## O> run
## O> sbin
## O> srv
## O> sys
## O> tmp
## O> usr
## O> var

Copy files into and out of containers

Just like docker cp, stevedore lets you copy files into and out of containers. The logic mimics the logic in the docker command line client as closely as possible.

To copy a file into our container x, use $cp_in

path <- tempfile()
writeLines("hello", path)
x$cp_in(path, "/hello")

And the new file is on the container

x$exec(c("cat", "/hello"), stream = FALSE)$output

## O> hello

The input can be a single file or a single directory.

To copy out, use $cp_out

dest <- tempfile()
x$cp_out("/usr/local/bin/iterate", dest)

Here is the iterate script, from the container:

writeLines(readLines(dest, n = 10))

## #!/bin/sh
## set -e
##
## if [ "$#" -ge 1 ]; then
##     TIMES=$1
## else
##     TIMES=10
## fi
##
## if [ "$#" -ge 2 ]; then

There is also a convenience method at the root of the docker object that behaves more like docker cp and requires that one of the source or destination arguments is given in <container>:<path> format:

src <- paste0(x$name(), ":/usr/local/bin/iterate")
src

## [1] "sad_ptolemy:/usr/local/bin/iterate"

dest2 <- tempfile()
docker$cp(src, dest2)

which achieves the same thing as the $cp_out command above.

unname(tools::md5sum(c(dest, dest2)))

## [1] "87bea4544cfd716dbab5030deb873b62" "87bea4544cfd716dbab5030deb873b62"

(don’t forget to remove your detached containers later!)

x$kill()

## NULL

Images

Pulling

Images can be directly pulled with docker$image$pull providing an image name (as either <repo> or <repo>:<tag>. If the image exists already this will be quick, and if the network connection is down then this will fail.

docker$image$pull("bash:latest")

## Pulling from library/bash latest
## Already exists 89d9c30c1d48
## Pulling fs layer 1cd014c0f09d
## Pulling fs layer fed606654955
## 1cd014c0f09d: Downloading 31.87 kB/3.17 MB 1%
## fed606654955: Downloading 340 B/340 B 100%
## Verifying Checksum fed606654955
## Download complete fed606654955
## 1cd014c0f09d: Downloading 228.48 kB/3.17 MB 7%
## 1cd014c0f09d: Downloading 588.92 kB/3.17 MB 19%
## 1cd014c0f09d: Downloading 1.08 MB/3.17 MB 34%
## 1cd014c0f09d: Downloading 1.41 MB/3.17 MB 44%
## 1cd014c0f09d: Downloading 1.75 MB/3.17 MB 55%
## 1cd014c0f09d: Downloading 2.08 MB/3.17 MB 65%
## 1cd014c0f09d: Downloading 2.42 MB/3.17 MB 76%
## 1cd014c0f09d: Downloading 2.75 MB/3.17 MB 87%
## 1cd014c0f09d: Downloading 3.07 MB/3.17 MB 97%
## Verifying Checksum 1cd014c0f09d
## Download complete 1cd014c0f09d
## 1cd014c0f09d: Extracting 32.77 kB/3.17 MB 1%
## 1cd014c0f09d: Extracting 262.14 kB/3.17 MB 8%
## 1cd014c0f09d: Extracting 2.16 MB/3.17 MB 68%
## 1cd014c0f09d: Extracting 2.98 MB/3.17 MB 94%
## 1cd014c0f09d: Extracting 3.05 MB/3.17 MB 96%
## 1cd014c0f09d: Extracting 3.15 MB/3.17 MB 99%
## 1cd014c0f09d: Extracting 3.17 MB/3.17 MB 100%
## Pull complete 1cd014c0f09d
## fed606654955: Extracting 340 B/340 B 100%
## fed606654955: Extracting 340 B/340 B 100%
## Pull complete fed606654955
## Digest: sha256:293ac2e5c5be7722d6f4aa620c6451aea359eec1f2f6d5c0faef948b86e449cd
## Status: Downloaded newer image for bash:latest

## <docker_image>
##   export()
##   help(help_type = getOption("help_type"))
##   history()
##   id()
##   inspect(reload = TRUE)
##   labels(reload = TRUE)
##   name()
##   reload()
##   remove(force = NULL, noprune = NULL)
##   short_id()
##   tag(repo, tag = NULL)
##   tags(reload = TRUE)
##   untag(repo_tag)

The object returned by pull is an image object - that can be

created by using `$get`

img <- docker$image$get("bash:latest")

Building

The other common way of getting images is to build them (the equivalent of docker build). So if we have a path (here, iterate) containing a Dockerfile:

dir("iterate")

## [1] "Dockerfile" "iterate"

The Dockerfile itself contains:

FROM alpine:latest
COPY iterate /usr/local/bin/iterate
CMD chmod +x /usr/local/bin/iterate
LABEL stevedore_version 0.0.1
ENTRYPOINT ["/usr/local/bin/iterate"]

and the iterate file is an executable shell script containing:

#!/bin/sh
set -e

if [ "$#" -ge 1 ]; then
    TIMES=$1
else
    TIMES=10
fi

if [ "$#" -ge 2 ]; then
    INTERVAL=$2
else
    INTERVAL=1
fi

echo "Doing $TIMES iterations with interval $INTERVAL"
i=0
while [ $i -lt $TIMES ]; do
    let i+=1
    echo "Iteration $i..."
    sleep $INTERVAL
done
echo "Done!"

We can build this image using:

img <- docker$image$build("iterate", tag = "richfitz/iterate", nocache = TRUE)

## Step 1/5 : FROM alpine:latest
##  ---> cc0abc535e36
## Step 2/5 : COPY iterate /usr/local/bin/iterate
##  ---> bfead14674a0
## Step 3/5 : CMD chmod +x /usr/local/bin/iterate
##  ---> Running in 3ffd8d1225b8
## Removing intermediate container 3ffd8d1225b8
##  ---> d5b6a0eaa685
## Step 4/5 : LABEL stevedore_version 0.0.1
##  ---> Running in c150ea2a1f95
## Removing intermediate container c150ea2a1f95
##  ---> 346745e9ebc8
## Step 5/5 : ENTRYPOINT ["/usr/local/bin/iterate"]
##  ---> Running in a17b554ff885
## Removing intermediate container a17b554ff885
##  ---> 244154bfbb99
## Successfully built 244154bfbb99
## Successfully tagged richfitz/iterate:latest

img

## <docker_image>
##   export()
##   help(help_type = getOption("help_type"))
##   history()
##   id()
##   inspect(reload = TRUE)
##   labels(reload = TRUE)
##   name()
##   reload()
##   remove(force = NULL, noprune = NULL)
##   short_id()
##   tag(repo, tag = NULL)
##   tags(reload = TRUE)
##   untag(repo_tag)

The newly created image is returned as an image object and can be used via $container$run()

invisible(
  docker$container$run(img, c("10", "0.1"), rm = TRUE, stream = stdout()))

## O> Doing 10 iterations with interval 0.1
## O> Iteration 1...
## O> Iteration 2...
## O> Iteration 3...
## O> Iteration 4...
## O> Iteration 5...
## O> Iteration 6...
## O> Iteration 7...
## O> Iteration 8...
## O> Iteration 9...
## O> Iteration 10...
## O> Done!

Importing

There is a third way of creating an image, which is to import it from a tar archive. This is not yet documented (TODO) but can be done via $image$import()

Working with image objects

Each image object has a number of methods.

img <- docker$image$get("richfitz/iterate")
img

## <docker_image>
##   export()
##   help(help_type = getOption("help_type"))
##   history()
##   id()
##   inspect(reload = TRUE)
##   labels(reload = TRUE)
##   name()
##   reload()
##   remove(force = NULL, noprune = NULL)
##   short_id()
##   tag(repo, tag = NULL)
##   tags(reload = TRUE)
##   untag(repo_tag)

The $id(), $short_id(), $labels(), $name() and $tags() query basic information about an image

img$id()

## [1] "sha256:244154bfbb9995fc3c5fede726ec4c2679ba393375f2a8130ffd8537dcce3285"

img$short_id()

## [1] "sha256:244154bfbb"

img$labels()

## stevedore_version
##           "0.0.1"

img$name()

## [1] "richfitz/iterate"

img$tags()

## [1] "richfitz/iterate:latest"

(short_idis always 10 characters long and does not include a leadingsha256:`).

The inspect() method returns detailed information about the image

img$inspect()

## $id
## [1] "sha256:244154bfbb9995fc3c5fede726ec4c2679ba393375f2a8130ffd8537dcce3285"
##
## $repo_tags
## [1] "richfitz/iterate:latest"
##
## $repo_digests
## character(0)
##
## $parent
## [1] "sha256:346745e9ebc8af6b623cdf5729ceddfd215e33d7886a7e72e71beba46d9bceca"
##
## $comment
## [1] ""
##
## $created
## [1] "2020-01-12T10:05:44.4499183Z"
##
## $container
## [1] "a17b554ff885999f2bd26d6716e358fea4d3e01194986dca3c0e6c4b57c095db"
##
## $container_config
## $container_config$hostname
## [1] "a17b554ff885"
##
## $container_config$domainname
## [1] ""
##
## $container_config$user
## [1] ""
##
## $container_config$attach_stdin
## [1] FALSE
##
## $container_config$attach_stdout
## [1] FALSE
##
## $container_config$attach_stderr
## [1] FALSE
##
## $container_config$exposed_ports
## NULL
##
## $container_config$tty
## [1] FALSE
##
## $container_config$open_stdin
## [1] FALSE
##
## $container_config$stdin_once
## [1] FALSE
##
## $container_config$env
## [1] "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
##
## $container_config$cmd
## [1] "/bin/sh"
## [2] "-c"
## [3] "#(nop) "
## [4] "ENTRYPOINT [\"/usr/local/bin/iterate\"]"
##
## $container_config$healthcheck
## NULL
##
## $container_config$args_escaped
## [1] TRUE
##
## $container_config$image
## [1] "sha256:346745e9ebc8af6b623cdf5729ceddfd215e33d7886a7e72e71beba46d9bceca"
##
## $container_config$volumes
## NULL
##
## $container_config$working_dir
## [1] ""
##
## $container_config$entrypoint
## [1] "/usr/local/bin/iterate"
##
## $container_config$network_disabled
## [1] NA
##
## $container_config$mac_address
## [1] NA
##
## $container_config$on_build
## character(0)
##
## $container_config$labels
## stevedore_version
##           "0.0.1"
##
## $container_config$stop_signal
## [1] NA
##
## $container_config$stop_timeout
## [1] NA
##
## $container_config$shell
## character(0)
##
##
## $docker_version
## [1] "18.09.2"
##
## $author
## [1] ""
##
## $config
## $config$hostname
## [1] ""
##
## $config$domainname
## [1] ""
##
## $config$user
## [1] ""
##
## $config$attach_stdin
## [1] FALSE
##
## $config$attach_stdout
## [1] FALSE
##
## $config$attach_stderr
## [1] FALSE
##
## $config$exposed_ports
## NULL
##
## $config$tty
## [1] FALSE
##
## $config$open_stdin
## [1] FALSE
##
## $config$stdin_once
## [1] FALSE
##
## $config$env
## [1] "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
##
## $config$cmd
## [1] "/bin/sh"                         "-c"
## [3] "chmod +x /usr/local/bin/iterate"
##
## $config$healthcheck
## NULL
##
## $config$args_escaped
## [1] TRUE
##
## $config$image
## [1] "sha256:346745e9ebc8af6b623cdf5729ceddfd215e33d7886a7e72e71beba46d9bceca"
##
## $config$volumes
## NULL
##
## $config$working_dir
## [1] ""
##
## $config$entrypoint
## [1] "/usr/local/bin/iterate"
##
## $config$network_disabled
## [1] NA
##
## $config$mac_address
## [1] NA
##
## $config$on_build
## character(0)
##
## $config$labels
## stevedore_version
##           "0.0.1"
##
## $config$stop_signal
## [1] NA
##
## $config$stop_timeout
## [1] NA
##
## $config$shell
## character(0)
##
##
## $architecture
## [1] "amd64"
##
## $os
## [1] "linux"
##
## $os_version
## [1] NA
##
## $size
## [1] 5591606
##
## $virtual_size
## [1] 5591606
##
## $graph_driver
## $graph_driver$name
## [1] "overlay2"
##
## $graph_driver$data
##                                                                                          lower_dir
##   "/var/lib/docker/overlay2/e1a21604d525ede2c5e9e6d59ac7dceb33bc7469ad98cc9997477a38c310305c/diff"
##                                                                                         merged_dir
## "/var/lib/docker/overlay2/934d66f90f6c661634b1618ea61d7f0b87149631cb4715059b862e18c27eac1f/merged"
##                                                                                          upper_dir
##   "/var/lib/docker/overlay2/934d66f90f6c661634b1618ea61d7f0b87149631cb4715059b862e18c27eac1f/diff"
##                                                                                           work_dir
##   "/var/lib/docker/overlay2/934d66f90f6c661634b1618ea61d7f0b87149631cb4715059b862e18c27eac1f/work"
##
##
## $root_fs
## $root_fs$type
## [1] "layers"
##
## $root_fs$layers
## [1] "sha256:6b27de954cca6332272e7709b7d8ceccee1489d9452af73391df360a26123580"
## [2] "sha256:14794d0f3100e41f9a96e1d181db26e010ae56489b484f0abcc782dcfc438de5"
##
## $root_fs$base_layer
## [1] NA
##
##
## $metadata
## $metadata$last_tag_time
## [1] "2020-01-12T10:05:44.5147212Z"

the exact format varies between docker API versions but should be the same for all images within an API version.

The history() method returns a data.frame of information about the history of an image (i.e., the layers that it is constructed from)

img$history()

##                                                                        id
## 1 sha256:244154bfbb9995fc3c5fede726ec4c2679ba393375f2a8130ffd8537dcce3285
## 2 sha256:346745e9ebc8af6b623cdf5729ceddfd215e33d7886a7e72e71beba46d9bceca
## 3 sha256:d5b6a0eaa685450861afb86bc00f05762bba84284ad2b36b252893f4c0972bb4
## 4 sha256:bfead14674a0cf29a4cb48ee5b11d006b7451ddd098086bc3866ded70821cd8d
## 5 sha256:cc0abc535e36a7ede71978ba2bbd8159b8a5420b91f2fbc520cdf5f673640a34
## 6                                                               <missing>
##      created
## 1 1578823544
## 2 1578823544
## 3 1578823543
## 4 1578823543
## 5 1577215212
## 6 1577215212
##                                                                                                                created_by
## 1                                                                /bin/sh -c #(nop)  ENTRYPOINT ["/usr/local/bin/iterate"]
## 2                                                                        /bin/sh -c #(nop)  LABEL stevedore_version=0.0.1
## 3                                               /bin/sh -c #(nop)  CMD ["/bin/sh" "-c" "chmod +x /usr/local/bin/iterate"]
## 4 /bin/sh -c #(nop) COPY file:8b8ba7864a94787016cc3c519efd97a1c7dde8a1b64fec3d078096872b2ece4c in /usr/local/bin/iterate
## 5                                                                                      /bin/sh -c #(nop)  CMD ["/bin/sh"]
## 6                       /bin/sh -c #(nop) ADD file:36fdc8cb08228a87093fb227736f4ce1d4d6c15366326dea541fbbd863976ee5 in /
##           tags    size comment
## 1 richfitz....       0
## 2                    0
## 3                    0
## 4                  306
## 5 alpine:l....       0
## 6              5591300

(printing these objects is a real challenge!).

The export() method exports an image as a tar object. There is some work still required to make this work nicely (currently it returns a [potentially long] raw vector).

There are several methods that operate to modify or destroy the image:

The $tag() method will tag an image, for example

img$tag("richfitz/iterate", "0.0.1")
img$reload()
img$tags()

## [1] "richfitz/iterate:0.0.1"  "richfitz/iterate:latest"

While the $untag() method will remove a tag

img$untag("richfitz/iterate:0.0.1")

The $remove() method will remove an image - this returns a data.frame indicating what actually happened (images are only actually deleted if there are no other tags pointing at an image and if noprune is not TRUE.

img$remove()

##                  untagged
## 1 richfitz/iterate:latest
## 2                    <NA>
## 3                    <NA>
## 4                    <NA>
## 5                    <NA>
## 6                    <NA>
##                                                                   deleted
## 1                                                                    <NA>
## 2 sha256:244154bfbb9995fc3c5fede726ec4c2679ba393375f2a8130ffd8537dcce3285
## 3 sha256:346745e9ebc8af6b623cdf5729ceddfd215e33d7886a7e72e71beba46d9bceca
## 4 sha256:d5b6a0eaa685450861afb86bc00f05762bba84284ad2b36b252893f4c0972bb4
## 5 sha256:bfead14674a0cf29a4cb48ee5b11d006b7451ddd098086bc3866ded70821cd8d
## 6 sha256:ce1557b8602d2427fb71296d2c6ab9b05103d830cdf2eb5d45cdfe25c3ed11dd

Volumes

Docker volumes provide a useful abstraction for interacting with (possibly persistent) file volumes across containers. To create a volume using stevedore (equivalent to docker volume create) use $volume$create():

vol <- docker$volume$create("myvolume")

Volumes can be listed:

docker$volume$list()

##                                                               name driver
## 1                                                         myvolume  local
## 2 dc5d8f843c0fefd3e0c6a729e7326fe262c94aa50a49065448d7ef664c53a285  local
##                                                                                       mountpoint
## 1                                                         /var/lib/docker/volumes/myvolume/_data
## 2 /var/lib/docker/volumes/dc5d8f843c0fefd3e0c6a729e7326fe262c94aa50a49065448d7ef664c53a285/_data
##             created_at status labels scope options usage_data
## 1 2020-01-12T10:05:47Z               local             NA, NA
## 2 2019-12-23T08:27:51Z               local             NA, NA

Working with volume objects

There’s very little that can be done with volume objects:

vol

## <docker_volume>
##   help(help_type = getOption("help_type"))
##   inspect(reload = TRUE)
##   map(path, readonly = FALSE)
##   name()
##   reload()
##   remove(force = NULL)

We can get the name:

vol$name()

## [1] "myvolume"

Inspect the metadata

vol$inspect()

## $name
## [1] "myvolume"
##
## $driver
## [1] "local"
##
## $mountpoint
## [1] "/var/lib/docker/volumes/myvolume/_data"
##
## $created_at
## [1] "2020-01-12T10:05:47Z"
##
## $status
## NULL
##
## $labels
## NULL
##
## $scope
## [1] "local"
##
## $options
## NULL
##
## $usage_data
## NULL

Generate mount definitions:

vol$map("/comtainer/path")

## [1] "myvolume:/comtainer/path"

and can remove the volume

vol$remove()

## NULL

everything else comes from using volumes with containers.

Containers are mounted the same way as from the docker command line - with a string in the form <host>:<container>. Here we can use the volume name on the host side, so saying <myvolume>:/myvolume mounts our volume at /myvolume within the container. This can be done easily with the $map() method.

vol <- docker$volume$create("myvolume")
docker$container$run(
  "alpine:latest",
  c("sh", "-c", "echo hello world > /myvolume/output"),
  volumes = vol$map("/myvolume"),
  rm = TRUE)

## <docker_run_output>
##   $container:
##     <docker_container>
##       id: 946dbe3f449dd8433847f1517af6106385ff1d31ed755f671ee10a732e31ac65
##       name: determined_easley
##
##   $logs:
##

(We use sh -c here so that the redirect operates within the container - the third argument is evaluated by the shell within the container and redirects the value that is echoed to a file.)

We can see the result of this by using a second container to read the file:

docker$container$run(
  "alpine:latest",
  c("cat", "/myvolume/output"),
  volumes = vol$map("/myvolume"),
  rm = TRUE)$logs

## O> hello world

## O> hello world

Networks

Docker “networks” make it easy to get containers communicating with each other without exposing ports to the host. To achive this, one creates a docker network, then create containers attached to that network (containers can also be attached to networks after creation).

nw <- docker$network$create("mynetwork")

Networks can be listed:

docker$network$list()

##        name
## 1      host
## 2 mynetwork
## 3      none
## 4    bridge
##                                                                 id
## 1 d5a076bd27b8f3a0963da06b5c149e6e7ab63ebe5649e124fdf8a22602b215c2
## 2 05492a54216e3b100caa82959b714897dd10dd0292ae82f730328c2d6d29b1bb
## 3 80bf98ad0e7fac320903a891936aa9680462769b37168e38b483c7ff9612bb2c
## 4 8b98e06edb0adb42f306a3d86d2f4f3d62b7a9d15279d7c44d37908c120df1ac
##                          created scope driver enable_ipv6         ipam
## 1 2019-03-09T11:06:26.652857909Z local   host       FALSE default,....
## 2   2020-01-12T10:05:50.1991445Z local bridge       FALSE default,....
## 3 2019-03-09T11:06:26.606552055Z local   null       FALSE default,....
## 4 2020-01-10T06:57:36.297181373Z local bridge       FALSE default,....
##   internal attachable ingress containers      options labels
## 1    FALSE      FALSE   FALSE
## 2    FALSE      FALSE   FALSE
## 3    FALSE      FALSE   FALSE
## 4    FALSE      FALSE   FALSE            true, tr....

The networks bridge, host and none always exist - they are special to docker.

Working with network objects

Like volume objects, network objects do very little themselves:

nw

## <docker_network>
##   connect(container = NULL, endpoint_config = NULL)
##   containers(reload = TRUE)
##   disconnect(container = NULL, force = NULL)
##   help(help_type = getOption("help_type"))
##   id()
##   inspect(reload = TRUE)
##   name(reload = TRUE)
##   reload()
##   remove()

The $name() and $id() methods get the name and id of the network

nw$name()

## [1] "mynetwork"

nw$id()

## [1] "05492a54216e3b100caa82959b714897dd10dd0292ae82f730328c2d6d29b1bb"

$inspect() gets detailed metadata

nw$inspect()

## $name
## [1] "mynetwork"
##
## $id
## [1] "05492a54216e3b100caa82959b714897dd10dd0292ae82f730328c2d6d29b1bb"
##
## $created
## [1] "2020-01-12T10:05:50.1991445Z"
##
## $scope
## [1] "local"
##
## $driver
## [1] "bridge"
##
## $enable_ipv6
## [1] FALSE
##
## $ipam
## $ipam$driver
## [1] "default"
##
## $ipam$config
## $ipam$config[[1]]
##          subnet         gateway
## "172.18.0.0/16"    "172.18.0.1"
##
##
## $ipam$options
## list()
##
##
## $internal
## [1] FALSE
##
## $attachable
## [1] FALSE
##
## $ingress
## [1] FALSE
##
## $containers
## list()
##
## $options
## character(0)
##
## $labels
## character(0)

$containers() lists containers attached to the network (currently an empty list - this network has no attached containers)

nw$containers()

## list()

$remove() removes the network

nw$remove()

## NULL

Generally you’ll want to put containers onto a network.

The setup here is to create a network, and then use the network argument to $container$run() to attach a container to that network. Once established, containers on the same network can use another docker container’s name as the hostname and communicate!

nw <- docker$network$create("mynetwork")
server <- docker$container$run("nginx", network = nw, name = "server",
                               detach = TRUE, rm = TRUE)
server$status()

## [1] "running"

Now we can attach other networks to this container and communicate with the server:

docker$container$run("alpine:latest", c("ping", "server", "-c", "3"),
                     network = nw, stream = stdout(), rm = TRUE)

## O> PING server (172.19.0.2): 56 data bytes
## O> 64 bytes from 172.19.0.2: seq=0 ttl=64 time=0.099 ms
## O> 64 bytes from 172.19.0.2: seq=1 ttl=64 time=0.208 ms
## O> 64 bytes from 172.19.0.2: seq=2 ttl=64 time=0.228 ms
## O>
## O> --- server ping statistics ---
## O> 3 packets transmitted, 3 packets received, 0% packet loss
## O> round-trip min/avg/max = 0.099/0.178/0.228 ms

## <docker_run_output>
##   $container:
##     <docker_container>
##       id: 36ee5c4501190e86eac95a52284cbfd69a22fe74d95088773f41627e3dc57c93
##       name: agitated_pasteur
##
##   $logs:
##     O> PING server (172.19.0.2): 56 data bytes
##     O> 64 bytes from 172.19.0.2: seq=0 ttl=64 time=0.099 ms
##     O> 64 bytes from 172.19.0.2: seq=1 ttl=64 time=0.208 ms
##     O> 64 bytes from 172.19.0.2: seq=2 ttl=64 time=0.228 ms
##     O>
##     O> --- server ping statistics ---
##     O> 3 packets transmitted, 3 packets received, 0% packet loss
##     O> round-trip min/avg/max = 0.099/0.178/0.228 ms

Omitting the network argument, the second container can’t find the server:

docker$container$run("alpine:latest", c("ping", "server", "-c", "3"),
                     stream = stdout(), rm = TRUE)

## E> ping: bad address 'server'

## Error: Command 'ping server -c 3' in image 'alpine:latest' returned non-zero exit status 1
## ping: bad address 'server'

The server container exposes a webserver on port 80. For containers on the network we can access this port:

res <- docker$container$run("richfitz/curl", c("curl", "-s", "http://server"),
                            network = nw, rm = TRUE)

## O> <!DOCTYPE html>
## O> <html>
## O> <head>
## O> <title>Welcome to nginx!</title>
## O> <style>
## O>     body {
## O>         width: 35em;
## O>         margin: 0 auto;
## O>         font-family: Tahoma, Verdana, Arial, sans-serif;
## O>     }
## O> </style>
## O> </head>
## O> <body>
## O> <h1>Welcome to nginx!</h1>
## O> <p>If you see this page, the nginx web server is successfully installed and
## O> working. Further configuration is required.</p>
## O>
## O> <p>For online documentation and support please refer to
## O> <a href="http://nginx.org/">nginx.org</a>.<br/>
## O> Commercial support is available at
## O> <a href="http://nginx.com/">nginx.com</a>.</p>
## O>
## O> <p><em>Thank you for using nginx.</em></p>
## O> </body>
## O> </html>

head(res$logs, 10)

##  [1] "<!DOCTYPE html>\n"
##  [2] "<html>\n"
##  [3] "<head>\n"
##  [4] "<title>Welcome to nginx!</title>\n"
##  [5] "<style>\n"
##  [6] "    body {\n"
##  [7] "        width: 35em;\n"
##  [8] "        margin: 0 auto;\n"
##  [9] "        font-family: Tahoma, Verdana, Arial, sans-serif;\n"
## [10] "    }\n"

server$stop()

## NULL

nw$remove()

## NULL

Other docker functions

There are a few functions at the top level of the docker_client object:

$ping() tests the connection to the server and reports the API version for the server - this is a (for docker) very fast function to use to test that things seem to be working.

docker$ping()

## [1] "OK"
## attr(,"api_version")
## [1] "1.39"
## attr(,"buildkit_version")
## [1] NA
## attr(,"docker_experimental")
## [1] FALSE

$api_version() reports the API version that the client is using (this can be varied from 1.25 to 1.39)

docker$api_version()

## [1] "1.39"

$version() reports detailed version information from the server:

docker$version()

## $platform
## $platform$name
## [1] "Docker Engine - Community"
##
##
## $components
##     name version      details
## 1 Engine 18.09.2 1.39, am....
##
## $version
## [1] "18.09.2"
##
## $api_version
## [1] "1.39"
##
## $min_api_version
## [1] "1.12"
##
## $git_commit
## [1] "6247962"
##
## $go_version
## [1] "go1.10.6"
##
## $os
## [1] "linux"
##
## $arch
## [1] "amd64"
##
## $kernel_version
## [1] "4.9.125-linuxkit"
##
## $experimental
## [1] NA
##
## $build_time
## [1] "2019-02-10T04:13:06.000000000+00:00"

$info() reports a bunch of other information about the state of the server (Docker describes this as “get system information” in its documentation) - this is equivalent to running docker info

docker$info()

## $id
## [1] "54B2:VUDF:CFVG:KTXY:5ZI6:S7NK:LQNM:7CFA:X6TH:5PRV:SUFC:ZDK4"
##
## $containers
## [1] 0
##
## $containers_running
## [1] 0
##
## $containers_paused
## [1] 0
##
## $containers_stopped
## [1] 0
##
## $images
## [1] 73
##
## $driver
## [1] "overlay2"
##
## $driver_status
## $driver_status[[1]]
## [1] "Backing Filesystem" "extfs"
##
## $driver_status[[2]]
## [1] "Supports d_type" "true"
##
## $driver_status[[3]]
## [1] "Native Overlay Diff" "true"
##
##
## $docker_root_dir
## [1] "/var/lib/docker"
##
## $system_status
## list()
##
## $plugins
## $plugins$volume
## [1] "local"
##
## $plugins$network
## [1] "bridge"  "host"    "macvlan" "null"    "overlay"
##
## $plugins$authorization
## character(0)
##
## $plugins$log
##  [1] "awslogs"    "fluentd"    "gcplogs"    "gelf"       "journald"
##  [6] "json-file"  "local"      "logentries" "splunk"     "syslog"
##
##
## $memory_limit
## [1] TRUE
##
## $swap_limit
## [1] TRUE
##
## $kernel_memory
## [1] TRUE
##
## $cpu_cfs_period
## [1] TRUE
##
## $cpu_cfs_quota
## [1] TRUE
##
## $cpu_shares
## [1] TRUE
##
## $cpu_set
## [1] TRUE
##
## $oom_kill_disable
## [1] TRUE
##
## $ipv4_forwarding
## [1] TRUE
##
## $bridge_nf_iptables
## [1] TRUE
##
## $bridge_nf_ip6tables
## [1] TRUE
##
## $debug
## [1] TRUE
##
## $n_fd
## [1] 26
##
## $n_goroutines
## [1] 53
##
## $system_time
## [1] "2020-01-12T10:06:01.1253405Z"
##
## $logging_driver
## [1] "json-file"
##
## $cgroup_driver
## [1] "cgroupfs"
##
## $n_events_listener
## [1] 2
##
## $kernel_version
## [1] "4.9.125-linuxkit"
##
## $operating_system
## [1] "Docker for Mac"
##
## $os_type
## [1] "linux"
##
## $architecture
## [1] "x86_64"
##
## $n_cpu
## [1] 2
##
## $mem_total
## [1] 2096164864
##
## $index_server_address
## [1] "https://index.docker.io/v1/"
##
## $registry_config
## $registry_config$allow_nondistributable_artifacts_cidrs
## character(0)
##
## $registry_config$allow_nondistributable_artifacts_hostnames
## character(0)
##
## $registry_config$insecure_registry_cidrs
## [1] "127.0.0.0/8"
##
## $registry_config$index_configs
## $registry_config$index_configs$docker.io
## $registry_config$index_configs$docker.io$name
## [1] "docker.io"
##
## $registry_config$index_configs$docker.io$mirrors
## character(0)
##
## $registry_config$index_configs$docker.io$secure
## [1] TRUE
##
## $registry_config$index_configs$docker.io$official
## [1] TRUE
##
##
##
## $registry_config$mirrors
## character(0)
##
##
## $generic_resources
## [1] named_resource_spec    discrete_resource_spec
## <0 rows> (or 0-length row.names)
##
## $http_proxy
## [1] "gateway.docker.internal:3128"
##
## $https_proxy
## [1] "gateway.docker.internal:3129"
##
## $no_proxy
## [1] ""
##
## $name
## [1] "linuxkit-025000000001"
##
## $labels
## character(0)
##
## $experimental_build
## [1] FALSE
##
## $server_version
## [1] "18.09.2"
##
## $cluster_store
## [1] ""
##
## $cluster_advertise
## [1] ""
##
## $runtimes
## $runtimes$runc
## $runtimes$runc$path
## [1] "runc"
##
## $runtimes$runc$runtime_args
## character(0)
##
##
##
## $default_runtime
## [1] "runc"
##
## $swarm
## $swarm$node_id
## [1] ""
##
## $swarm$node_addr
## [1] ""
##
## $swarm$local_node_state
## [1] "inactive"
##
## $swarm$control_available
## [1] FALSE
##
## $swarm$error
## [1] ""
##
## $swarm$remote_managers
## [1] node_id addr
## <0 rows> (or 0-length row.names)
##
## $swarm$nodes
## [1] NA
##
## $swarm$managers
## [1] NA
##
## $swarm$cluster
## NULL
##
##
## $live_restore_enabled
## [1] FALSE
##
## $isolation
## [1] ""
##
## $init_binary
## [1] "docker-init"
##
## $containerd_commit
## $containerd_commit$id
## [1] "9754871865f7fe2f4e74d43e2fc7ccd237edcbce"
##
## $containerd_commit$expected
## [1] "9754871865f7fe2f4e74d43e2fc7ccd237edcbce"
##
##
## $runc_commit
## $runc_commit$id
## [1] "09c8266bf2fcf9519a651b04ae54c967b9ab86ec"
##
## $runc_commit$expected
## [1] "09c8266bf2fcf9519a651b04ae54c967b9ab86ec"
##
##
## $init_commit
## $init_commit$id
## [1] "fec3683"
##
## $init_commit$expected
## [1] "fec3683"
##
##
## $security_options
## [1] "name=seccomp,profile=default"
##
## $product_license
## [1] "Community Engine"
##
## $warnings
## character(0)

Finally, $df() will return information about resource and data usage by docker - all containers, networks, volumes, etc.

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.

Using docker with stevedore

Rich FitzJohn

2020-01-12

Containers

Working with containers

Run commands in running containers with exec

Copy files into and out of containers

Images

Pulling

The object returned by pull is an image object - that can be

created by using $get

Building

Importing

Working with image objects

Volumes

Working with volume objects

Networks

Working with network objects

Other docker functions

Run commands in running containers with `exec`

created by using `$get`