Commands

yaml

type: "io.kestra.plugin.scripts.r.Commands"

Execute R scripts from the Command Line Interface.

Examples

Create an R script, install required packages and execute it. Note that instead of defining the script inline, you could create the script as a dedicated R script in the embedded VS Code editor and point to its location by path. If you do so, make sure to enable namespace files by setting the enabled flag of the namespaceFiles property to true.

yaml

id: r_commands
namespace: company.team

tasks:
  - id: r
    type: io.kestra.plugin.scripts.r.Commands
    inputFiles:
      main.R: |
        library(lubridate)
        ymd("20100604");
        mdy("06-04-2011");
        dmy("04/06/2012")
    beforeCommands:
      - Rscript -e 'install.packages("lubridate")'
    commands:
      - Rscript main.R

Properties

`commands`

Type: array
SubType: string
Dynamic: ✔️
Required: ✔️
Min items: 1

The commands to run

`interpreter`

Type: array
SubType: string
Dynamic: ❌
Required: ✔️
Default: [/bin/sh, -c]
Min items: 1

Which interpreter to use.

`warningOnStdErr`

Type: boolean
Dynamic: ❌
Required: ✔️
Default: true

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

`beforeCommands`

Type: array
SubType: string
Dynamic: ✔️
Required: ❌

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: ✔️
Required: ❌
Default: r-base

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

`docker`

⚠ Deprecated

Type: DockerOptions
Dynamic: ❓
Required: ❌

Deprecated - use the 'taskRunner' property instead.

Only used if the taskRunner property is not set

`env`

Type: object
SubType: string
Dynamic: ✔️
Required: ❌

Additional environment variables for the current process.

`failFast`

Type: boolean
Dynamic: ❌
Required: ❌
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. You can also disable it if your interpreter does not support the set -eoption.

`inputFiles`

Type:
- object
- string
Dynamic: ✔️
Required: ❌

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

`namespaceFiles`

Type: NamespaceFiles
Dynamic: ❌
Required: ❌

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`

⚠ Deprecated

Type: boolean
Dynamic: ❓
Required: ❌
Default: false

Whether to setup the output directory mechanism.

Required to use the {{ outputDir }} expression. Note that it could increase the starting time. Deprecated, use the outputFiles property instead.

`outputFiles`

Type: array
SubType: string
Dynamic: ✔️
Required: ❌

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.

`runner`

⚠ Deprecated

Type: string
Dynamic: ❌
Required: ❌
Possible Values:
- PROCESS
- DOCKER

Deprecated - use the 'taskRunner' property instead.

Only used if the taskRunner property is not set

`targetOS`

Type: string
Dynamic: ❓
Required: ❌
Default: AUTO
Possible Values:
- LINUX
- WINDOWS
- AUTO

The target operating system where the script will run.

`taskRunner`

Type: TaskRunner
Dynamic: ❌
Required: ❌
Default: {type=io.kestra.plugin.scripts.runner.docker.Docker}

The task runner to use.

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

Outputs

`exitCode`

Type: integer
Required: ✔️
Default: 0

The exit code of the entire flow execution.

`outputFiles`

Type: object
SubType: string
Required: ❌

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

`vars`

Type: object
Required: ❌

The value extracted from the output of the executed commands.

Definitions

`io.kestra.core.models.tasks.NamespaceFiles`

Properties

`enabled`

Type: boolean
Dynamic: ❌
Required: ❌
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: ❌
Required: ❌

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: ❌
Required: ❌

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: ❌
Required: ❌

The maximum amount of CPU resources a container can use.

Make sure to set that to a numeric value e.g. cpus: "1.5" or cpus: "4" or 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`

Properties

`type`

Type: string
Dynamic: ❓
Required: ✔️
Validation regExp: \p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*(\.\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*)*
Min length: 1

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

Properties

`kernelMemory`

Type: string
Dynamic: ✔️
Required: ❌

The maximum amount of kernel memory the container can use.

The minimum allowed value is 4MB. 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 the kernel-memory docs for more details.

`memory`

Type: string
Dynamic: ✔️
Required: ❌

The maximum amount of memory resources the container can use.

Make sure to use the format number + unit (regardless of the case) without any spaces. The unit can be KB (kilobytes), MB (megabytes), GB (gigabytes), etc.

Given that it's case-insensitive, the following values are equivalent:

"512MB"
"512Mb"
"512mb"
"512000KB"
"0.5GB"

It is recommended that you allocate at least 6MB.

`memoryReservation`

Type: string
Dynamic: ✔️
Required: ❌

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 doesn’t exceed the limit.

`memorySwap`

Type: string
Dynamic: ✔️
Required: ❌

The total amount of memory and swap that can be used by a container.

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

`memorySwappiness`

Type: string
Dynamic: ✔️
Required: ❌

A setting which controls the likelihood of the kernel to swap memory pages.

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: ❌
Required: ❌

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 system’s processes to free the memory.

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

Properties

`image`

Type: string
Dynamic: ✔️
Required: ✔️
Min length: 1

Docker image to use.

`config`

Type:
- string
- object
Dynamic: ✔️
Required: ❌

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: ❌
Required: ❌

Limits the CPU usage to a given maximum threshold value.

By default, each container’s access to the host machine’s CPU cycles is unlimited. You can set various constraints to limit a given container’s access to the host machine’s CPU cycles.

`credentials`

Type: Credentials
Dynamic: ✔️
Required: ❌

`deviceRequests`

Type: array
SubType: DeviceRequest
Dynamic: ❌
Required: ❌

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

`entryPoint`

Type: array
SubType: string
Dynamic: ✔️
Required: ❌

Docker entrypoint to use.

`extraHosts`

Type: array
SubType: string
Dynamic: ✔️
Required: ❌

Extra hostname mappings to the container network interface configuration.

`host`

Type: string
Dynamic: ✔️
Required: ❌

Docker API URI.

`memory`

Type: Memory
Dynamic: ❌
Required: ❌

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: ✔️
Required: ❌

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

`pullPolicy`

Type: string
Dynamic: ❌
Required: ❌
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: ✔️
Required: ❌

Size of /dev/shm in bytes.

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

`user`

Type: string
Dynamic: ✔️
Required: ❌

User in the Docker container.

`volumes`

Type: array
SubType: string
Dynamic: ✔️
Required: ❌

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: ✔️
Required: ❌

The registry authentication.

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

`identityToken`

Type: string
Dynamic: ✔️
Required: ❌

The identity token.

`password`

Type: string
Dynamic: ✔️
Required: ❌

The registry password.

`registry`

Type: string
Dynamic: ✔️
Required: ❌

The registry URL.

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

`registryToken`

Type: string
Dynamic: ✔️
Required: ❌

The registry token.

`username`

Type: string
Dynamic: ✔️
Required: ❌

The registry username.

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

Properties

`capabilities`

Type: array
SubType: array
Dynamic: ❌
Required: ❌

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

`count`

Type: integer
Dynamic: ❌
Required: ❌

`deviceIds`

Type: array
SubType: string
Dynamic: ✔️
Required: ❌

`driver`

Type: string
Dynamic: ✔️
Required: ❌

`options`

Type: object
SubType: string
Dynamic: ❌
Required: ❌

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

These options are passed directly to the driver.

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​Commands

Commands

enabled

exclude

include

cpus

type

kernelMemory

memory

memoryReservation

memorySwap

memorySwappiness

oomKillDisable

image

config

cpu

credentials

deviceRequests

entryPoint

extraHosts

host

memory

networkMode

pullPolicy

shmSize

user

volumes

auth

identityToken

password

registry

registryToken

username

capabilities

count

deviceIds

driver

options

Commands

`enabled`

`exclude`

`include`

`cpus`

`type`

`kernelMemory`

`memory`

`memoryReservation`

`memorySwap`

`memorySwappiness`

`oomKillDisable`

`image`

`config`

`cpu`

`credentials`

`deviceRequests`

`entryPoint`

`extraHosts`

`host`

`memory`

`networkMode`

`pullPolicy`

`shmSize`

`user`

`volumes`

`auth`

`identityToken`

`password`

`registry`

`registryToken`

`username`

`capabilities`

`count`

`deviceIds`

`driver`

`options`