Script Script

yaml
type: "io.kestra.plugin.scripts.r.Script"

Execute an R script.

Examples

Install a package and execute an R script

yaml
id: "script"
type: "io.kestra.plugin.scripts.r.Script"
script: |
  library(lubridate)
  ymd("20100604");
  mdy("06-04-2011");
  dmy("04/06/2012")
beforeCommands:
  - Rscript -e 'install.packages("lubridate")'

Add an R script in the embedded VS Code editor, install required packages and execute it.

Here is an example R script that you can add in the embedded VS Code editor. You can name the script file main.R:

r
library(dplyr)
library(arrow)

data(mtcars) # load mtcars data
print(head(mtcars))

final <- mtcars %>%
    summarise(
    avg_mpg = mean(mpg),
    avg_disp = mean(disp),
    avg_hp = mean(hp),
    avg_drat = mean(drat),
    avg_wt = mean(wt),
    avg_qsec = mean(qsec),
    avg_vs = mean(vs),
    avg_am = mean(am),
    avg_gear = mean(gear),
    avg_carb = mean(carb)
    )
final %>% print()
write.csv(final, "final.csv")

mtcars_clean <- na.omit(mtcars) # this line removes rows with NA values
write_parquet(mtcars_clean, "mtcars_clean.parquet")

Note that tasks in Kestra are stateless. Therefore, the files generated by a task, such as the CSV and Parquet files in the example above, are not persisted in Kestra's internal storage, unless you explicitly tell Kestra to do so. Make sure to add the outputFiles property to your task as shown below to persist the generated Parquet file (or any other file) in Kestra's internal storage and make them visible in the Outputs tab.

To access this output in downstream tasks, use the syntax . Alternatively, you can wrap your tasks that need to pass data between each other in a WorkingDirectory task โ€” this way, those tasks will share the same working directory and will be able to access the same files.

Note how we use the read function to read the content of the R script stored as a Namespace File.

Finally, note that the docker property is optional. If you don't specify it, Kestra will use the default R image. If you want to use a different image, you can specify it in the docker property as shown below.

yaml
id: rCars
namespace: dev
tasks:
  - id: r
    type: io.kestra.plugin.scripts.r.Script
    warningOnStdErr: false
    docker:
      image: ghcr.io/kestra-io/rdata:latest
    script: "{{ read('main.R') }}
    outputFiles:
      - "*.csv"
      - "*.parquet"

Properties

interpreter

  • Type: array
  • SubType: string
  • Dynamic: โŒ
  • Required: โœ”๏ธ
  • Default: [/bin/sh, -c]
  • Min items: 1

Which interpreter to use.

runner

  • Type: string
  • Dynamic: โŒ
  • Required: โœ”๏ธ
  • Default: DOCKER
  • Possible Values:
    • PROCESS
    • DOCKER

The task runner to use โ€” by default, Kestra runs all scripts in DOCKER.

Only used if the taskRunner property is not set

script

  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โœ”๏ธ
  • Min length: 1

The inline script content. This property is intended for the script file's content as a (multiline) string, not a path to a file. To run a command from a file such as Rscript main.R or python main.py, use the corresponding Commands task for a given language instead.

warningOnStdErr

  • Type: boolean
  • Dynamic: โŒ
  • Required: โœ”๏ธ
  • Default: true

Whether to set the task state to WARNING if any stdErr is emitted.

beforeCommands

  • Type: array
  • SubType: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

A list of commands that will run before the commands, allowing to set up the environment e.g. pip install -r requirements.txt.

containerImage

  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ
  • Default: r-base

The task runner container image, only used if the task runner is container-based.

docker

  • Type: DockerOptions
  • Dynamic: โŒ
  • Required: โŒ
  • Default: {image=r-base, pullPolicy=ALWAYS}

Docker options when using the DOCKER runner

env

  • Type: object
  • SubType: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

Additional environment variables for the current process.

failFast

  • Type: boolean
  • Dynamic: โŒ
  • Required: โŒ
  • Default: true

Fail the task on the first command with a non-zero status.

If set to false all commands will be executed one after the other. The final state of task execution is determined by the last command. Note that this property maybe be ignored if a non compatible interpreter is specified.

inputFiles

  • Type:
    • object
    • string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The files to create on the local filesystem. It can be a map or a JSON object.

namespaceFiles

Inject namespace files.

Inject namespace files to this task. When enabled, it will, by default, load all namespace files into the working directory. However, you can use the include or exclude properties to limit which namespace files will be injected.

outputDirectory

  • Type: boolean
  • Dynamic: โ“
  • Required: โŒ
  • Default: false

Whether to setup the output directory mechanism.

Required to use the expression. Note that it could increase the starting time.

outputFiles

  • Type: array
  • SubType: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The files from the local filesystem to send to Kestra's internal storage.

Must be a list of glob expressions relative to the current working directory, some examples: my-dir/**, my-dir/*/** or my-dir/my-file.txt.

taskRunner

The task runner to use.

Task runners are provided by plugins, each have their own properties.

Outputs

exitCode

  • Type: integer
  • Dynamic: โ“
  • Required: โœ”๏ธ
  • Default: 0

The exit code of the entire flow execution.

outputFiles

  • Type: object
  • SubType: string
  • Dynamic: โŒ
  • Required: โŒ

The output files' URIs in Kestra's internal storage.

vars

  • Type: object
  • Dynamic: โ“
  • Required: โŒ

The value extracted from the output of the executed commands.

Definitions

io.kestra.core.models.tasks.NamespaceFiles

Properties

enabled
  • Type: boolean
  • Dynamic: โŒ
  • Required: โŒ
  • Default: true

Whether to enable namespace files to be loaded into the working directory. If explicitly set to true in a task, it will load all Namespace Files into the task's working directory. Note that this property is by default set to true so that you can specify only the include and exclude properties to filter the files to load without having to explicitly set enabled to true.

exclude
  • Type: array
  • SubType: string
  • Dynamic: โŒ
  • Required: โŒ

A list of filters to exclude matching glob patterns. This allows you to exclude a subset of the Namespace Files from being downloaded at runtime. You can combine this property together with include to only inject a subset of files that you need into the task's working directory.

include
  • Type: array
  • SubType: string
  • Dynamic: โŒ
  • Required: โŒ

A list of filters to include only matching glob patterns. This allows you to only load a subset of the Namespace Files into the working directory.

io.kestra.plugin.scripts.runner.docker.Cpu

Properties

cpus
  • Type: integer
  • Dynamic: โŒ
  • Required: โŒ

The maximum amount of CPU resources a container can use.

For instance, if the host machine has two CPUs and you set cpus:"1.5", the container is guaranteed at most one and a half of the CPUs.

io.kestra.core.models.tasks.runners.TaskRunner

io.kestra.plugin.scripts.runner.docker.Memory

Properties

kernelMemory
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The maximum amount of kernel memory the container can use.

The minimum allowed value is 4m. Because kernel memory cannot be swapped out, a container which is starved of kernel memory may block host machine resources, which can have side effects on the host machine and on other containers. See --kernel-memory details.

memory
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The maximum amount of memory resources the container can use.

It is recommended that you set the value to at least 6 megabytes.

memoryReservation
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

Allows you to specify a soft limit smaller than memory which is activated when Docker detects contention or low memory on the host machine.

If you use memoryReservation, it must be set lower than memory for it to take precedence. Because it is a soft limit, it does not guarantee that the container doesnโ€™t exceed the limit.

memorySwap
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The amount of memory this container is allowed to swap to disk.

If memory and memorySwap are set to the same value, this prevents containers from using any swap. This is because memorySwap is the amount of combined memory and swap that can be used, while memory is only the amount of physical memory that can be used.

memorySwappiness
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The amount of memory this container is allowed to swap to disk.

By default, the host kernel can swap out a percentage of anonymous pages used by a container. You can set memorySwappiness to a value between 0 and 100, to tune this percentage.

oomKillDisable
  • Type: boolean
  • Dynamic: โŒ
  • Required: โŒ

By default, if an out-of-memory (OOM) error occurs, the kernel kills processes in a container.

To change this behavior, use the oomKillDisable option. Only disable the OOM killer on containers where you have also set the memory option. If the memory flag is not set, the host can run out of memory, and the kernel may need to kill the host systemโ€™s processes to free the memory.

io.kestra.plugin.scripts.exec.scripts.models.DockerOptions

Properties

image
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โœ”๏ธ
  • Min length: 1

Docker image to use.

config
  • Type:
    • string
    • object
  • Dynamic: โœ”๏ธ
  • Required: โŒ

Docker configuration file.

Docker configuration file that can set access credentials to private container registries. Usually located in ~/.docker/config.json.

cpu
  • Type: Cpu
  • Dynamic: โŒ
  • Required: โŒ

Limits the CPU usage to a given maximum threshold value.

By default, each containerโ€™s access to the host machineโ€™s CPU cycles is unlimited. You can set various constraints to limit a given containerโ€™s access to the host machineโ€™s CPU cycles.

credentials
  • Type: Credentials
  • Dynamic: โœ”๏ธ
  • Required: โŒ
deviceRequests
  • Type: array
  • SubType: DeviceRequest
  • Dynamic: โŒ
  • Required: โŒ

A list of device requests to be sent to device drivers.

entryPoint
  • Type: array
  • SubType: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

Docker entrypoint to use.

extraHosts
  • Type: array
  • SubType: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

Extra hostname mappings to the container network interface configuration.

host
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

Docker API URI.

memory
  • Type: Memory
  • Dynamic: โŒ
  • Required: โŒ

Limits memory usage to a given maximum threshold value.

Docker can enforce hard memory limits, which allow the container to use no more than a given amount of user or system memory, or soft limits, which allow the container to use as much memory as it needs unless certain conditions are met, such as when the kernel detects low memory or contention on the host machine. Some of these options have different effects when used alone or when more than one option is set.

networkMode
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

Docker network mode to use e.g. host, none, etc.

pullPolicy
  • Type: string
  • Dynamic: โŒ
  • Required: โŒ
  • Default: ALWAYS
  • Possible Values:
    • IF_NOT_PRESENT
    • ALWAYS
    • NEVER

The image pull policy for a container image and the tag of the image, which affect when Docker attempts to pull (download) the specified image.

shmSize
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

Size of /dev/shm in bytes.

The size must be greater than 0. If omitted, the system uses 64MB.

user
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

User in the Docker container.

volumes
  • Type: array
  • SubType: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

List of volumes to mount.

Must be a valid mount expression as string, example : /home/user:/app.

Volumes mount are disabled by default for security reasons; you must enable them on server configuration by setting kestra.tasks.scripts.docker.volume-enabled to true.

io.kestra.plugin.scripts.runner.docker.Credentials

Properties

auth
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The registry authentication.

The auth field is a base64-encoded authentication string of username:password or a token.

identityToken
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The identity token.

password
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The registry password.

registry
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The registry URL.

If not defined, the registry will be extracted from the image name.

registryToken
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The registry token.

username
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ

The registry username.

io.kestra.plugin.scripts.runner.docker.DeviceRequest

Properties

capabilities
  • Type: array
  • SubType: array
  • Dynamic: โŒ
  • Required: โŒ

A list of capabilities; an OR list of AND lists of capabilities.

count
  • Type: integer
  • Dynamic: โŒ
  • Required: โŒ
deviceIds
  • Type: array
  • SubType: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ
driver
  • Type: string
  • Dynamic: โœ”๏ธ
  • Required: โŒ
options
  • Type: object
  • SubType: string
  • Dynamic: โŒ
  • Required: โŒ

Driver-specific options, specified as key/value pairs.

These options are passed directly to the driver.

Was this page helpful?