com.google.api.services.genomics.v2alpha1.model

Class Action

java.lang.Object

java.util.AbstractMap<String,Object>

com.google.api.client.util.GenericData

com.google.api.client.json.GenericJson

com.google.api.services.genomics.v2alpha1.model.Action

All Implemented Interfaces:

Cloneable, Map<String,Object>

public final class Action
extends GenericJson

Specifies a single action that runs a Docker container.

This is the Java data model class that specifies how to parse/serialize into the JSON that is transmitted over HTTP when working with the Genomics API. For a detailed explanation see: https://developers.google.com/api-client-library/java/google-http-java-client/json

Author:

Google, Inc.

Nested Class Summary

Nested classes/interfaces inherited from class com.google.api.client.util.GenericData

GenericData.Flags

Nested classes/interfaces inherited from class java.util.AbstractMap

AbstractMap.SimpleEntry<K,V>, AbstractMap.SimpleImmutableEntry<K,V>

Nested classes/interfaces inherited from interface java.util.Map

Map.Entry<K,V>

Constructor Summary

Constructors

Constructor and Description
Action()

Method Summary

Modifier and Type	Method and Description
Action	clone()
List<String>	getCommands() If specified, overrides the `CMD` specified in the container.
Secret	getCredentials() If the specified image is hosted on a private registry other than Google Container Registry, the credentials required to pull the image must be specified here as an encrypted secret.
String	getEntrypoint() If specified, overrides the `ENTRYPOINT` specified in the container.
Map<String,String>	getEnvironment() The environment to pass into the container.
List<String>	getFlags() The set of flags to apply to this action.
String	getImageUri() Required.
Map<String,String>	getLabels() Labels to associate with the action.
List<Mount>	getMounts() A list of mounts to make available to the action.
String	getName() An optional name for the container.
String	getPidNamespace() An optional identifier for a PID namespace to run the action inside.
Map<String,Integer>	getPortMappings() A map of containers to host port mappings for this container.
String	getTimeout() The maximum amount of time to give the action to complete.
Action	set(String fieldName, Object value)
Action	setCommands(List<String> commands) If specified, overrides the `CMD` specified in the container.
Action	setCredentials(Secret credentials) If the specified image is hosted on a private registry other than Google Container Registry, the credentials required to pull the image must be specified here as an encrypted secret.
Action	setEntrypoint(String entrypoint) If specified, overrides the `ENTRYPOINT` specified in the container.
Action	setEnvironment(Map<String,String> environment) The environment to pass into the container.
Action	setFlags(List<String> flags) The set of flags to apply to this action.
Action	setImageUri(String imageUri) Required.
Action	setLabels(Map<String,String> labels) Labels to associate with the action.
Action	setMounts(List<Mount> mounts) A list of mounts to make available to the action.
Action	setName(String name) An optional name for the container.
Action	setPidNamespace(String pidNamespace) An optional identifier for a PID namespace to run the action inside.
Action	setPortMappings(Map<String,Integer> portMappings) A map of containers to host port mappings for this container.
Action	setTimeout(String timeout) The maximum amount of time to give the action to complete.

Methods inherited from class com.google.api.client.json.GenericJson

getFactory, setFactory, toPrettyString, toString

Methods inherited from class com.google.api.client.util.GenericData

entrySet, equals, get, getClassInfo, getUnknownKeys, hashCode, put, putAll, remove, setUnknownKeys

Methods inherited from class java.util.AbstractMap

clear, containsKey, containsValue, isEmpty, keySet, size, values

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

compute, computeIfAbsent, computeIfPresent, forEach, getOrDefault, merge, putIfAbsent, remove, replace, replace, replaceAll

Constructor Detail

Action

public Action()

Method Detail

getCommands

public List<String> getCommands()

If specified, overrides the `CMD` specified in the container. If the container also has an `ENTRYPOINT` the values are used as entrypoint arguments. Otherwise, they are used as a command and arguments to run inside the container.

Returns:

value or null for none

setCommands

public Action setCommands(List<String> commands)

If specified, overrides the `CMD` specified in the container. If the container also has an `ENTRYPOINT` the values are used as entrypoint arguments. Otherwise, they are used as a command and arguments to run inside the container.

Parameters:

commands - commands or null for none

getCredentials

public Secret getCredentials()

If the specified image is hosted on a private registry other than Google Container Registry, the credentials required to pull the image must be specified here as an encrypted secret. The secret must decrypt to a JSON-encoded dictionary containing both `username` and `password` keys.

Returns:

value or null for none

setCredentials

public Action setCredentials(Secret credentials)

If the specified image is hosted on a private registry other than Google Container Registry, the credentials required to pull the image must be specified here as an encrypted secret. The secret must decrypt to a JSON-encoded dictionary containing both `username` and `password` keys.

Parameters:

credentials - credentials or null for none

getEntrypoint

public String getEntrypoint()

If specified, overrides the `ENTRYPOINT` specified in the container.

Returns:

value or null for none

setEntrypoint

public Action setEntrypoint(String entrypoint)

If specified, overrides the `ENTRYPOINT` specified in the container.

Parameters:

entrypoint - entrypoint or null for none

getEnvironment

public Map<String,String> getEnvironment()

The environment to pass into the container. This environment is merged with values specified in the google.genomics.v2alpha1.Pipeline message, overwriting any duplicate values. In addition to the values passed here, a few other values are automatically injected into the environment. These cannot be hidden or overwritten. `GOOGLE_PIPELINE_FAILED` will be set to "1" if the pipeline failed because an action has exited with a non-zero status (and did not have the `IGNORE_EXIT_STATUS` flag set). This can be used to determine if additional debug or logging actions should execute. `GOOGLE_LAST_EXIT_STATUS` will be set to the exit status of the last non-background action that executed. This can be used by workflow engine authors to determine whether an individual action has succeeded or failed.

Returns:

value or null for none

setEnvironment

public Action setEnvironment(Map<String,String> environment)

The environment to pass into the container. This environment is merged with values specified in the google.genomics.v2alpha1.Pipeline message, overwriting any duplicate values. In addition to the values passed here, a few other values are automatically injected into the environment. These cannot be hidden or overwritten. `GOOGLE_PIPELINE_FAILED` will be set to "1" if the pipeline failed because an action has exited with a non-zero status (and did not have the `IGNORE_EXIT_STATUS` flag set). This can be used to determine if additional debug or logging actions should execute. `GOOGLE_LAST_EXIT_STATUS` will be set to the exit status of the last non-background action that executed. This can be used by workflow engine authors to determine whether an individual action has succeeded or failed.

Parameters:

environment - environment or null for none

getFlags

public List<String> getFlags()

The set of flags to apply to this action.

Returns:

value or null for none

setFlags

public Action setFlags(List<String> flags)

The set of flags to apply to this action.

Parameters:

flags - flags or null for none

getImageUri

public String getImageUri()

Required. The URI to pull the container image from. Note that all images referenced by actions in the pipeline are pulled before the first action runs. If multiple actions reference the same image, it is only pulled once, ensuring that the same image is used for all actions in a single pipeline. The image URI can be either a complete host and image specification (e.g., quay.io/biocontainers/samtools), a library and image name (e.g., google/cloud-sdk) or a bare image name ('bash') to pull from the default library. No schema is required in any of these cases. If the specified image is not public, the service account specified for the Virtual Machine must have access to pull the images from GCR, or appropriate credentials must be specified in the google.genomics.v2alpha1.Action.credentials field.

Returns:

value or null for none

setImageUri

public Action setImageUri(String imageUri)

Required. The URI to pull the container image from. Note that all images referenced by actions in the pipeline are pulled before the first action runs. If multiple actions reference the same image, it is only pulled once, ensuring that the same image is used for all actions in a single pipeline. The image URI can be either a complete host and image specification (e.g., quay.io/biocontainers/samtools), a library and image name (e.g., google/cloud-sdk) or a bare image name ('bash') to pull from the default library. No schema is required in any of these cases. If the specified image is not public, the service account specified for the Virtual Machine must have access to pull the images from GCR, or appropriate credentials must be specified in the google.genomics.v2alpha1.Action.credentials field.

Parameters:

imageUri - imageUri or null for none

getLabels

public Map<String,String> getLabels()

Labels to associate with the action. This field is provided to assist workflow engine authors in identifying actions (for example, to indicate what sort of action they perform, such as localization or debugging). They are returned in the operation metadata, but are otherwise ignored.

Returns:

value or null for none

setLabels

public Action setLabels(Map<String,String> labels)

Labels to associate with the action. This field is provided to assist workflow engine authors in identifying actions (for example, to indicate what sort of action they perform, such as localization or debugging). They are returned in the operation metadata, but are otherwise ignored.

Parameters:

labels - labels or null for none

getMounts

public List<Mount> getMounts()

A list of mounts to make available to the action. In addition to the values specified here, every action has a special virtual disk mounted under `/google` that contains log files and other operational components. /google/logs All logs written during the pipeline execution. /google/logs/output The combined standard output and standard error of all actions run as part of the pipeline execution. /google/logs/action/stdout The complete contents of each individual action's standard output. /google/logs/action/stderr The complete contents of each individual action's standard error output.

Returns:

value or null for none

setMounts

public Action setMounts(List<Mount> mounts)

A list of mounts to make available to the action. In addition to the values specified here, every action has a special virtual disk mounted under `/google` that contains log files and other operational components. /google/logs All logs written during the pipeline execution. /google/logs/output The combined standard output and standard error of all actions run as part of the pipeline execution. /google/logs/action/stdout The complete contents of each individual action's standard output. /google/logs/action/stderr The complete contents of each individual action's standard error output.

Parameters:

mounts - mounts or null for none

getName

public String getName()

An optional name for the container. The container hostname will be set to this name, making it useful for inter-container communication. The name must contain only upper and lowercase alphanumeric characters and hypens and cannot start with a hyphen.

Returns:

value or null for none

setName

public Action setName(String name)

An optional name for the container. The container hostname will be set to this name, making it useful for inter-container communication. The name must contain only upper and lowercase alphanumeric characters and hypens and cannot start with a hyphen.

Parameters:

name - name or null for none

getPidNamespace

public String getPidNamespace()

An optional identifier for a PID namespace to run the action inside. Multiple actions should use the same string to share a namespace. If unspecified, a separate isolated namespace is used.

Returns:

value or null for none

setPidNamespace

public Action setPidNamespace(String pidNamespace)

An optional identifier for a PID namespace to run the action inside. Multiple actions should use the same string to share a namespace. If unspecified, a separate isolated namespace is used.

Parameters:

pidNamespace - pidNamespace or null for none

getPortMappings

public Map<String,Integer> getPortMappings()

A map of containers to host port mappings for this container. If the container already specifies exposed ports, use the `PUBLISH_EXPOSED_PORTS` flag instead. The host port number must be less than 65536. If it is zero, an unused random port is assigned. To determine the resulting port number, consult the `ContainerStartedEvent` in the operation metadata.

Returns:

value or null for none

setPortMappings

public Action setPortMappings(Map<String,Integer> portMappings)

A map of containers to host port mappings for this container. If the container already specifies exposed ports, use the `PUBLISH_EXPOSED_PORTS` flag instead. The host port number must be less than 65536. If it is zero, an unused random port is assigned. To determine the resulting port number, consult the `ContainerStartedEvent` in the operation metadata.

Parameters:

portMappings - portMappings or null for none

getTimeout

public String getTimeout()

The maximum amount of time to give the action to complete. If the action fails to complete before the timeout, it will be terminated and the exit status will be non-zero. The pipeline will continue or terminate based on the rules defined by the `ALWAYS_RUN` and `IGNORE_EXIT_STATUS` flags.

Returns:

value or null for none

setTimeout

public Action setTimeout(String timeout)

The maximum amount of time to give the action to complete. If the action fails to complete before the timeout, it will be terminated and the exit status will be non-zero. The pipeline will continue or terminate based on the rules defined by the `ALWAYS_RUN` and `IGNORE_EXIT_STATUS` flags.

Parameters:

timeout - timeout or null for none

set

public Action set(String fieldName,
                  Object value)

Overrides:

set in class GenericJson

clone

public Action clone()

Overrides:

clone in class GenericJson