As of January 1, 2020 this library no longer supports Python 2 on the latest released version. Library versions released prior to that date will continue to be available. For more information please visit Python 2 support on Google Cloud.

Types for Google Cloud Lifesciences v2beta API¶

class google.cloud.lifesciences_v2beta.types.Accelerator(mapping=None, *, ignore_unknown_fields=False, **kwargs)[source]¶

Bases: proto.message.Message

Carries information about an accelerator that can be attached to a VM.

type_¶

The accelerator type string (for example, “nvidia-tesla-t4”).

Only NVIDIA GPU accelerators are currently supported. If an NVIDIA GPU is attached, the required runtime libraries will be made available to all containers under /usr/local/nvidia. The driver version to install must be specified using the NVIDIA driver version parameter on the virtual machine specification. Note that attaching a GPU increases the worker VM startup time by a few minutes.

Type: str

count¶

How many accelerators of this type to attach.

Type: int

class google.cloud.lifesciences_v2beta.types.Action(mapping=None, *, ignore_unknown_fields=False, **kwargs)[source]¶

Bases: proto.message.Message

Specifies a single action that runs a Docker container.

container_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 hyphens and cannot start with a hyphen.

Type: str

image_uri¶

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.cloud.lifesciences.v2beta.Action.credentials][google.cloud.lifesciences.v2beta.Action.credentials] field.

Type: str

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.

Type: MutableSequence[str]

entrypoint¶

If specified, overrides the ENTRYPOINT specified in the container.

Type: str

environment¶

The environment to pass into the container. This environment is merged with values specified in the [google.cloud.lifesciences.v2beta.Pipeline][google.cloud.lifesciences.v2beta.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.

Type: MutableMapping[str, str]

encrypted_environment¶

The encrypted environment to pass into the container. This environment is merged with values specified in the [google.cloud.lifesciences.v2beta.Pipeline][google.cloud.lifesciences.v2beta.Pipeline] message, overwriting any duplicate values.

The secret must decrypt to a JSON-encoded dictionary where key-value pairs serve as environment variable names and their values. The decoded environment variables can overwrite the values specified by the environment field.

Type: google.cloud.lifesciences_v2beta.types.Secret

pid_namespace¶

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.

Type: str

port_mappings¶

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.

Type: MutableMapping[int, int]

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.

Type: MutableSequence[google.cloud.lifesciences_v2beta.types.Mount]

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.

Type: MutableMapping[str, str]

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.

Type: google.cloud.lifesciences_v2beta.types.Secret

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.

Type: google.protobuf.duration_pb2.Duration

ignore_exit_status¶

Normally, a non-zero exit status causes the pipeline to fail. This flag allows execution of other actions to continue instead.

Type: bool

run_in_background¶

This flag allows an action to continue running in the background while executing subsequent actions. This is useful to provide services to other actions (or to provide debugging support tools like SSH servers).

Type: bool

always_run¶

By default, after an action fails, no further actions are run. This flag indicates that this action must be run even if the pipeline has already failed. This is useful for actions that copy output files off of the VM or for debugging. Note that no actions will be run if image prefetching fails.

Type: bool

enable_fuse¶

Enable access to the FUSE device for this action. Filesystems can then be mounted into disks shared with other actions. The other actions do not need the enable_fuse flag to access the mounted filesystem.

This has the effect of causing the container to be executed with CAP_SYS_ADMIN and exposes /dev/fuse to the container, so use it only for containers you trust.

Type: bool

publish_exposed_ports¶

Exposes all ports specified by EXPOSE statements in the container. To discover the host side port numbers, consult the ACTION_STARTED event in the operation metadata.

Type: bool

disable_image_prefetch¶

All container images are typically downloaded before any actions are executed. This helps prevent typos in URIs or issues like lack of disk space from wasting large amounts of compute resources.

If set, this flag prevents the worker from downloading the image until just before the action is executed.

Type: bool

disable_standard_error_capture¶

A small portion of the container’s standard error stream is typically captured and returned inside the ContainerStoppedEvent. Setting this flag disables this functionality.

Type: bool

block_external_network¶

Prevents the container from accessing the external network.

Type: bool

class EnvironmentEntry(mapping=None, *, ignore_unknown_fields=False, **kwargs)¶: Bases: proto.message.Message

class LabelsEntry(mapping=None, *, ignore_unknown_fields=False, **kwargs)¶: Bases: proto.message.Message

class PortMappingsEntry(mapping=None, *, ignore_unknown_fields=False, **kwargs)¶: Bases: proto.message.Message

class google.cloud.lifesciences_v2beta.types.ContainerKilledEvent(mapping=None, *, ignore_unknown_fields=False, **kwargs)[source]¶

Bases: proto.message.Message

An event generated when a container is forcibly terminated by the worker. Currently, this only occurs when the container outlives the timeout specified by the user.

action_id¶

The numeric ID of the action that started the container.

Type: int

class google.cloud.lifesciences_v2beta.types.ContainerStartedEvent(mapping=None, *, ignore_unknown_fields=False, **kwargs)[source]¶

Bases: proto.message.Message

An event generated when a container starts.

action_id¶

The numeric ID of the action that started this container.

Type: int

port_mappings¶

The container-to-host port mappings installed for this container. This set will contain any ports exposed using the PUBLISH_EXPOSED_PORTS flag as well as any specified in the Action definition.

Type: MutableMapping[int, int]

ip_address¶

The public IP address that can be used to connect to the container. This field is only populated when at least one port mapping is present. If the instance was created with a private address, this field will be empty even if port mappings exist.

Type: str

class PortMappingsEntry(mapping=None, *, ignore_unknown_fields=False, **kwargs)¶: Bases: proto.message.Message

class google.cloud.lifesciences_v2beta.types.ContainerStoppedEvent(mapping=None, *, ignore_unknown_fields=False, **kwargs)[source]¶

Bases: proto.message.Message

An event generated when a container exits.

action_id¶

The numeric ID of the action that started this container.

Type: int

exit_status¶

The exit status of the container.

Type: int

stderr¶

The tail end of any content written to standard error by the container. If the content emits large amounts of debugging noise or contains sensitive information, you can prevent the content from being printed by setting the DISABLE_STANDARD_ERROR_CAPTURE flag.

Note that only a small amount of the end of the stream is captured here. The entire stream is stored in the /google/logs directory mounted into each action, and can be copied off the machine as described elsewhere.

Type: str

class google.cloud.lifesciences_v2beta.types.DelayedEvent(mapping=None, *, ignore_unknown_fields=False, **kwargs)[source]¶

Bases: proto.message.Message

An event generated whenever a resource limitation or transient error delays execution of a pipeline that was otherwise ready to run.

cause¶

A textual description of the cause of the delay. The string can change without notice because it is often generated by another service (such as Compute Engine).

Type: str

metrics¶

If the delay was caused by a resource shortage, this field lists the Compute Engine metrics that are preventing this operation from running (for example, CPUS or INSTANCES). If the particular metric is not known, a single UNKNOWN metric will be present.

Type: MutableSequence[str]

class google.cloud.lifesciences_v2beta.types.Disk(mapping=None, *, ignore_unknown_fields=False, **kwargs)[source]¶

Bases: proto.message.Message

Carries information about a disk that can be attached to a VM.

See https://cloud.google.com/compute/docs/disks/performance for more information about disk type, size, and performance considerations.

Specify either [Volume][google.cloud.lifesciences.v2beta.Volume] or [Disk][google.cloud.lifesciences.v2beta.Disk], but not both.

name¶

A user-supplied name for the disk. Used when mounting the disk into actions. The name must contain only upper and lowercase alphanumeric characters and hyphens and cannot start with a hyphen.

Type: str

size_gb¶

The size, in GB, of the disk to attach. If the size is not specified, a default is chosen to ensure reasonable I/O performance.

If the disk type is specified as local-ssd, multiple local drives are automatically combined to provide the requested size. Note, however, that each physical SSD is 375GB in size, and no more than 8 drives can be attached to a single instance.

Type: int

type_¶

The Compute Engine disk type. If unspecified, pd-standard is used.

Type: str

source_image¶

An optional image to put on the disk before attaching it to the VM.

Type: str

class google.cloud.lifesciences_v2beta.types.Event(mapping=None, *, ignore_unknown_fields=False, **kwargs)[source]¶

Bases: proto.message.Message

Carries information about events that occur during pipeline execution.

This message has oneof fields (mutually exclusive fields). For each oneof, at most one member field can be set at the same time. Setting any member of the oneof automatically clears all other members.

timestamp¶

The time at which the event occurred.

Type: google.protobuf.timestamp_pb2.Timestamp

description¶

A human-readable description of the event. Note that these strings can change at any time without notice. Any application logic must use the information in the details field.

Type: str

delayed¶

See [google.cloud.lifesciences.v2beta.DelayedEvent][google.cloud.lifesciences.v2beta.DelayedEvent].