chore: regens API reference docs (#889)
diff --git a/docs/dyn/genomics_v2alpha1.pipelines.html b/docs/dyn/genomics_v2alpha1.pipelines.html
index 2c0c941..20a17af 100644
--- a/docs/dyn/genomics_v2alpha1.pipelines.html
+++ b/docs/dyn/genomics_v2alpha1.pipelines.html
@@ -75,12 +75,16 @@
<h1><a href="genomics_v2alpha1.html">Genomics API</a> . <a href="genomics_v2alpha1.pipelines.html">pipelines</a></h1>
<h2>Instance Methods</h2>
<p class="toc_element">
- <code><a href="#run">run(body, x__xgafv=None)</a></code></p>
-<p class="firstline">Runs a pipeline.</p>
+ <code><a href="#run">run(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(body, x__xgafv=None)</code>
- <pre>Runs a pipeline.
+ <code class="details" id="run">run(body=None, x__xgafv=None)</code>
+ <pre>Runs a pipeline. The returned Operation's metadata field will contain a
+google.genomics.v2alpha1.Metadata object describing the status of the
+pipeline execution. The [response] field will contain a
+google.genomics.v2alpha1.RunPipelineResponse object if the pipeline
+completes successfully.
**Note:** Before you can use this method, the Genomics Service Agent
must have access to your project. This is done automatically when the
@@ -96,116 +100,18 @@
[1]: /genomics/gsa
Args:
- body: object, The request body. (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 Genomics service
# account or the request will fail.
- "pipeline": { # Specifies a series of actions to execute, expressed as Docker containers. # The description of the pipeline to run.
+ "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",
},
- "actions": [ # The list of actions to execute, in the order they are specified.
- { # Specifies a single action that runs a Docker container.
- "environment": { # The environment to pass into the container. This environment is merged
- # with any values specified in the `Pipeline` message. These values
- # overwrite any in the `Pipeline` message.
- #
- # 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",
- },
- "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",
- ],
- "name": "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 hypens
- # and cannot start with a hyphen.
- "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",
- },
- "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.
- "imageUri": "A String", # 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.
- "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,
- },
- "flags": [ # The set of flags to apply to this action.
- "A String",
- ],
- "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.
- "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.
- "path": "A String", # The path to mount the disk inside the container.
- "readOnly": True or False, # If true, the disk is mounted read-only inside the container.
- "disk": "A String", # The name of the disk to mount, as specified in the resources section.
- },
- ],
- "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.
- "cipherText": "A String", # The value of the cipherText response from the `encrypt` method. This field
- # is intentionally unaudited.
- "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.
- },
- "entrypoint": "A String", # If specified, overrides the `ENTRYPOINT` specified in the container.
- },
- ],
"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.
@@ -227,15 +133,26 @@
#
# For more information about the effect of this parameter, see
# https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform.
- "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 on VM labels
- # imposed by Compute Engine.
- #
- # 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",
- },
- "machineType": "A String", # The machine type of the virtual machine to create. Must be the short name
+ "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.
+ "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.
+ "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 hypens and cannot start with a hyphen.
+ },
+ ],
+ "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
@@ -268,29 +185,21 @@
# 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.
- "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.
- "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.
- "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 hypens and cannot start with a hyphen.
- },
- ],
+ "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",
+ },
"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.
"scopes": [ # List of scopes to be enabled for this service account on the VM, in
- # addition to the Cloud Genomics API scope.
+ # addition to the cloud-platform API scope that will be added by default.
"A String",
],
"email": "A String", # Email address of the service account. If not specified, the default
@@ -336,6 +245,114 @@
# will be set to DEADLINE_EXCEEDED.
#
# If unspecified, it will default to 7 days.
+ "actions": [ # The list of actions to execute, in the order they are specified.
+ { # Specifies a single action that runs a Docker container.
+ "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,
+ },
+ "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",
+ ],
+ "name": "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 hypens
+ # and cannot start with a hyphen.
+ "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",
+ },
+ "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.genomics.v2alpha1.Action.credentials field.
+ "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.
+ "a_key": "A String",
+ },
+ "flags": [ # The set of flags to apply to this action.
+ "A String",
+ ],
+ "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.
+ "cipherText": "A String", # The value of the cipherText response from the `encrypt` method. This field
+ # is intentionally unaudited.
+ "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.
+ },
+ "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.
+ "path": "A String", # The path to mount the disk inside the container.
+ "readOnly": True or False, # If true, the disk is mounted read-only inside the container.
+ "disk": "A String", # The name of the disk to mount, as specified in the resources section.
+ },
+ ],
+ "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.
+ "entrypoint": "A String", # If specified, overrides the `ENTRYPOINT` specified in the container.
+ },
+ ],
},
"labels": { # User-defined labels to associate with the returned operation. These
# labels are not propagated to any Google Cloud Platform resources used by
@@ -357,16 +374,16 @@
{ # 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.
+ },
"metadata": { # An OperationMetadata or 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.
- "response": { # An Empty object.
- "a_key": "", # Properties of the object. Contains field @type with type URL.
- },
- "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
+ "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example&#58; `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
"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