docs: docs update (#911)
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Fixes #<issue_number_goes_here> 🦕
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+<h1><a href="lifesciences_v2beta.html">Cloud Life Sciences API</a> . <a href="lifesciences_v2beta.projects.html">projects</a> . <a href="lifesciences_v2beta.projects.locations.html">locations</a> . <a href="lifesciences_v2beta.projects.locations.pipelines.html">pipelines</a></h1>
+<h2>Instance Methods</h2>
+<p class="toc_element">
+ <code><a href="#run">run(parent, body=None, x__xgafv=None)</a></code></p>
+<p class="firstline">Runs a pipeline. The returned Operation's metadata field will contain a</p>
+<h3>Method Details</h3>
+<div class="method">
+ <code class="details" id="run">run(parent, body=None, x__xgafv=None)</code>
+ <pre>Runs a pipeline. The returned Operation's metadata field will contain a
+google.cloud.lifesciences.v2beta.Metadata object describing the status
+of the pipeline execution. The
+response field will contain a
+google.cloud.lifesciences.v2beta.RunPipelineResponse object if the
+pipeline completes successfully.
+
+**Note:** Before you can use this method, the *Life Sciences Service Agent*
+must have access to your project. This is done automatically when the
+Cloud Life Sciences API is first enabled, but if you delete this permission
+you must disable and re-enable the API to grant the Life Sciences
+Service Agent the required permissions.
+Authorization requires the following [Google
+IAM](https://cloud.google.com/iam/) permission:
+
+* `lifesciences.workflows.run`
+
+Args:
+ parent: string, The project and location that this request should be executed against. (required)
+ body: object, The request body.
+ The object takes the form of:
+
+{ # The arguments to the `RunPipeline` method. The requesting user must have
+ # the `iam.serviceAccounts.actAs` permission for the Cloud Life Sciences
+ # service account or the request will fail.
+ "labels": { # User-defined labels to associate with the returned operation. These
+ # labels are not propagated to any Google Cloud Platform resources used by
+ # the operation, and can be modified at any time.
+ #
+ # To associate labels with resources created while executing the operation,
+ # see the appropriate resource message (for example, `VirtualMachine`).
+ "a_key": "A String",
+ },
+ "pipeline": { # Specifies a series of actions to execute, expressed as Docker containers. # Required. The description of the pipeline to run.
+ "environment": { # The environment to pass into every action. Each action can also specify
+ # additional environment variables but cannot delete an entry from this map
+ # (though they can overwrite it with a different value).
+ "a_key": "A String",
+ },
+ "timeout": "A String", # The maximum amount of time to give the pipeline to complete. This includes
+ # the time spent waiting for a worker to be allocated. If the pipeline fails
+ # to complete before the timeout, it will be cancelled and the error code
+ # will be set to DEADLINE_EXCEEDED.
+ #
+ # If unspecified, it will default to 7 days.
+ "resources": { # The system resources for the pipeline run. # The resources required for execution.
+ #
+ # At least one zone or region must be specified or the pipeline run will fail.
+ "virtualMachine": { # Carries information about a Compute Engine VM resource. # The virtual machine specification.
+ "network": { # VM networking options. # The VM network configuration.
+ "subnetwork": "A String", # If the specified network is configured for custom subnet creation, the
+ # name of the subnetwork to attach the instance to must be specified here.
+ #
+ # The value is prefixed with `regions/*/subnetworks/` unless it contains a
+ # `/`, in which case it is assumed to be a fully specified subnetwork
+ # resource URL.
+ #
+ # If the `*` character appears in the value, it is replaced with the region
+ # that the virtual machine has been allocated in.
+ "network": "A String", # The network name to attach the VM's network interface to. The value will
+ # be prefixed with `global/networks/` unless it contains a `/`, in which
+ # case it is assumed to be a fully specified network resource URL.
+ #
+ # If unspecified, the global default network is used.
+ "usePrivateAddress": True or False, # If set to true, do not attach a public IP address to the VM. Note that
+ # without a public IP address, additional configuration is required to
+ # allow the VM to access Google services.
+ #
+ # See https://cloud.google.com/vpc/docs/configure-private-google-access
+ # for more information.
+ },
+ "bootDiskSizeGb": 42, # The size of the boot disk, in GB. The boot disk must be large
+ # enough to accommodate all of the Docker images from each action in the
+ # pipeline at the same time. If not specified, a small but reasonable
+ # default value is used.
+ "nvidiaDriverVersion": "A String", # The NVIDIA driver version to use when attaching an NVIDIA GPU accelerator.
+ # The version specified here must be compatible with the GPU libraries
+ # contained in the container being executed, and must be one of the drivers
+ # hosted in the `nvidia-drivers-us-public` bucket on Google Cloud Storage.
+ "labels": { # Optional set of labels to apply to the VM and any attached disk resources.
+ # These labels must adhere to the [name and value
+ # restrictions](https://cloud.google.com/compute/docs/labeling-resources) on
+ # VM labels imposed by Compute Engine.
+ #
+ # Labels keys with the prefix 'google-' are reserved for use by Google.
+ #
+ # Labels applied at creation time to the VM. Applied on a best-effort basis
+ # to attached disk resources shortly after VM creation.
+ "a_key": "A String",
+ },
+ "enableStackdriverMonitoring": True or False, # Whether Stackdriver monitoring should be enabled on the VM.
+ "cpuPlatform": "A String", # The CPU platform to request. An instance based on a newer platform can be
+ # allocated, but never one with fewer capabilities. The value of this
+ # parameter must be a valid Compute Engine CPU platform name (such as "Intel
+ # Skylake"). This parameter is only useful for carefully optimized work
+ # loads where the CPU platform has a significant impact.
+ #
+ # For more information about the effect of this parameter, see
+ # https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform.
+ "accelerators": [ # The list of accelerators to attach to the VM.
+ { # Carries information about an accelerator that can be attached to a VM.
+ "count": "A String", # How many accelerators of this type to attach.
+ "type": "A String", # The accelerator type string (for example, "nvidia-tesla-k80").
+ #
+ # 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.
+ },
+ ],
+ "machineType": "A String", # Required. The machine type of the virtual machine to create. Must be the short name
+ # of a standard machine type (such as "n1-standard-1") or a custom machine
+ # type (such as "custom-1-4096", where "1" indicates the number of vCPUs and
+ # "4096" indicates the memory in MB). See
+ # [Creating an instance with a custom machine
+ # type](https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type#create)
+ # for more specifications on creating a custom machine type.
+ "preemptible": True or False, # If true, allocate a preemptible VM.
+ "disks": [ # The list of disks to create and attach to the VM.
+ { # 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.
+ "sizeGb": 42, # 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.
+ "name": "A String", # 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": "A String", # The Compute Engine disk type. If unspecified, `pd-standard` is used.
+ "sourceImage": "A String", # An optional image to put on the disk before attaching it to the VM.
+ },
+ ],
+ "serviceAccount": { # Carries information about a Google Cloud service account. # The service account to install on the VM. This account does not need
+ # any permissions other than those required by the pipeline.
+ "email": "A String", # Email address of the service account. If not specified, the default
+ # Compute Engine service account for the project will be used.
+ "scopes": [ # List of scopes to be enabled for this service account on the VM, in
+ # addition to the cloud-platform API scope that will be added by default.
+ "A String",
+ ],
+ },
+ "bootImage": "A String", # The host operating system image to use.
+ #
+ # Currently, only Container-Optimized OS images can be used.
+ #
+ # The default value is `projects/cos-cloud/global/images/family/cos-stable`,
+ # which selects the latest stable release of Container-Optimized OS.
+ #
+ # This option is provided to allow testing against the beta release of the
+ # operating system to ensure that the new version does not interact
+ # negatively with production pipelines.
+ #
+ # To test a pipeline against the beta release of Container-Optimized OS,
+ # use the value `projects/cos-cloud/global/images/family/cos-beta`.
+ },
+ "regions": [ # The list of regions allowed for VM allocation. If set, the `zones` field
+ # must not be set.
+ "A String",
+ ],
+ "zones": [ # The list of zones allowed for VM allocation. If set, the `regions` field
+ # must not be set.
+ "A String",
+ ],
+ },
+ "actions": [ # The list of actions to execute, in the order they are specified.
+ { # Specifies a single action that runs a Docker container.
+ "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.
+ #
+ # <ul>
+ # <li><code>/google/logs</code> All logs written during the pipeline
+ # execution.</li>
+ # <li><code>/google/logs/output</code> The combined standard output and
+ # standard error of all actions run as part of the pipeline
+ # execution.</li>
+ # <li><code>/google/logs/action/*/stdout</code> The complete contents of
+ # each individual action's standard output.</li>
+ # <li><code>/google/logs/action/*/stderr</code> The complete contents of
+ # each individual action's standard error output.</li>
+ # </ul>
+ { # Carries information about a particular disk mount inside a container.
+ "disk": "A String", # The name of the disk to mount, as specified in the resources section.
+ "readOnly": True or False, # If true, the disk is mounted read-only inside the container.
+ "path": "A String", # The path to mount the disk inside the container.
+ },
+ ],
+ "publishExposedPorts": True or False, # 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.
+ "timeout": "A String", # 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.
+ "credentials": { # Holds encrypted information that is only decrypted and stored in RAM # 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.
+ # by the worker VM when running the pipeline.
+ "keyName": "A String", # The name of the Cloud KMS key that will be used to decrypt the secret
+ # value. The VM service account must have the required permissions and
+ # authentication scopes to invoke the `decrypt` method on the specified key.
+ "cipherText": "A String", # The value of the cipherText response from the `encrypt` method. This field
+ # is intentionally unaudited.
+ },
+ "imageUri": "A String", # 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 field.
+ "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.
+ "A String",
+ ],
+ "ignoreExitStatus": True or False, # Normally, a non-zero exit status causes the pipeline to fail. This flag
+ # allows execution of other actions to continue instead.
+ "runInBackground": True or False, # 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).
+ "enableFuse": True or False, # 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.
+ "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.
+ "a_key": "A String",
+ },
+ "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.
+ "a_key": 42,
+ },
+ "environment": { # The environment to pass into the container. This environment is merged
+ # with values specified in the 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.
+ "a_key": "A String",
+ },
+ "containerName": "A String", # 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.
+ "disableImagePrefetch": True or False, # 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.
+ "entrypoint": "A String", # If specified, overrides the `ENTRYPOINT` specified in the container.
+ "alwaysRun": True or False, # 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.
+ "disableStandardErrorCapture": True or False, # A small portion of the container's standard error stream is typically
+ # captured and returned inside the `ContainerStoppedEvent`. Setting this
+ # flag disables this functionality.
+ "pidNamespace": "A String", # 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.
+ },
+ ],
+ },
+ }
+
+ x__xgafv: string, V1 error format.
+ Allowed values
+ 1 - v1 error format
+ 2 - v2 error format
+
+Returns:
+ An object of the form:
+
+ { # This resource represents a long-running operation that is the result of a
+ # network API call.
+ "response": { # An Empty object.
+ "a_key": "", # Properties of the object. Contains field @type with type URL.
+ },
+ "name": "A String", # The server-assigned name for the operation. This may be passed to the other operation methods to retrieve information about the operation's status.
+ "error": { # The `Status` type defines a logical error model that is suitable for # The error result of the operation in case of failure or cancellation.
+ # different programming environments, including REST APIs and RPC APIs. It is
+ # used by [gRPC](https://github.com/grpc). Each `Status` message contains
+ # three pieces of data: error code, error message, and error details.
+ #
+ # You can find out more about this error model and how to work with it in the
+ # [API Design Guide](https://cloud.google.com/apis/design/errors).
+ "message": "A String", # A developer-facing error message, which should be in English. Any
+ # user-facing error message should be localized and sent in the
+ # google.rpc.Status.details field, or localized by the client.
+ "details": [ # A list of messages that carry the error details. There is a common set of
+ # message types for APIs to use.
+ {
+ "a_key": "", # Properties of the object. Contains field @type with type URL.
+ },
+ ],
+ "code": 42, # The status code, which should be an enum value of google.rpc.Code.
+ },
+ "metadata": { # An Metadata object. This will always be returned with the Operation.
+ "a_key": "", # Properties of the object. Contains field @type with type URL.
+ },
+ "done": True or False, # If the value is `false`, it means the operation is still in progress.
+ # If `true`, the operation is completed, and either `error` or `response` is
+ # available.
+ }</pre>
+</div>
+
+</body></html>
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