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75<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>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="#run">run(parent, body=None, x__xgafv=None)</a></code></p>
79<p class="firstline">Runs a pipeline. The returned Operation's metadata field will contain a</p>
80<h3>Method Details</h3>
81<div class="method">
82 <code class="details" id="run">run(parent, body=None, x__xgafv=None)</code>
83 <pre>Runs a pipeline. The returned Operation&#x27;s metadata field will contain a
84google.cloud.lifesciences.v2beta.Metadata object describing the status
85of the pipeline execution. The
86response field will contain a
87google.cloud.lifesciences.v2beta.RunPipelineResponse object if the
88pipeline completes successfully.
89
90**Note:** Before you can use this method, the *Life Sciences Service Agent*
91must have access to your project. This is done automatically when the
92Cloud Life Sciences API is first enabled, but if you delete this permission
93you must disable and re-enable the API to grant the Life Sciences
94Service Agent the required permissions.
95Authorization requires the following [Google
96IAM](https://cloud.google.com/iam/) permission:
97
98* `lifesciences.workflows.run`
99
100Args:
101 parent: string, The project and location that this request should be executed against. (required)
102 body: object, The request body.
103 The object takes the form of:
104
105{ # The arguments to the `RunPipeline` method. The requesting user must have
106 # the `iam.serviceAccounts.actAs` permission for the Cloud Life Sciences
107 # service account or the request will fail.
Bu Sun Kim65020912020-05-20 12:08:20 -0700108 &quot;pipeline&quot;: { # Specifies a series of actions to execute, expressed as Docker containers. # Required. The description of the pipeline to run.
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700109 &quot;environment&quot;: { # The environment to pass into every action. Each action can also specify
110 # additional environment variables but cannot delete an entry from this map
111 # (though they can overwrite it with a different value).
112 &quot;a_key&quot;: &quot;A String&quot;,
113 },
114 &quot;actions&quot;: [ # The list of actions to execute, in the order they are specified.
115 { # Specifies a single action that runs a Docker container.
116 &quot;publishExposedPorts&quot;: True or False, # Exposes all ports specified by `EXPOSE` statements in the container. To
117 # discover the host side port numbers, consult the `ACTION_STARTED` event
118 # in the operation metadata.
119 &quot;environment&quot;: { # The environment to pass into the container. This environment is merged
120 # with values specified in the google.cloud.lifesciences.v2beta.Pipeline
121 # message, overwriting any duplicate values.
122 #
123 # In addition to the values passed here, a few other values are
124 # automatically injected into the environment. These cannot be hidden or
125 # overwritten.
126 #
127 # `GOOGLE_PIPELINE_FAILED` will be set to &quot;1&quot; if the pipeline failed
128 # because an action has exited with a non-zero status (and did not have the
129 # `IGNORE_EXIT_STATUS` flag set). This can be used to determine if additional
130 # debug or logging actions should execute.
131 #
132 # `GOOGLE_LAST_EXIT_STATUS` will be set to the exit status of the last
133 # non-background action that executed. This can be used by workflow engine
134 # authors to determine whether an individual action has succeeded or failed.
135 &quot;a_key&quot;: &quot;A String&quot;,
136 },
137 &quot;labels&quot;: { # Labels to associate with the action. This field is provided to assist
138 # workflow engine authors in identifying actions (for example, to indicate
139 # what sort of action they perform, such as localization or debugging).
140 # They are returned in the operation metadata, but are otherwise ignored.
141 &quot;a_key&quot;: &quot;A String&quot;,
142 },
143 &quot;containerName&quot;: &quot;A String&quot;, # An optional name for the container. The container hostname will be set to
144 # this name, making it useful for inter-container communication. The name
145 # must contain only upper and lowercase alphanumeric characters and hyphens
146 # and cannot start with a hyphen.
147 &quot;commands&quot;: [ # If specified, overrides the `CMD` specified in the container. If the
148 # container also has an `ENTRYPOINT` the values are used as entrypoint
149 # arguments. Otherwise, they are used as a command and arguments to run
150 # inside the container.
151 &quot;A String&quot;,
152 ],
153 &quot;enableFuse&quot;: True or False, # Enable access to the FUSE device for this action. Filesystems can then
154 # be mounted into disks shared with other actions. The other actions do
155 # not need the `enable_fuse` flag to access the mounted filesystem.
156 #
157 # This has the effect of causing the container to be executed with
158 # `CAP_SYS_ADMIN` and exposes `/dev/fuse` to the container, so use it only
159 # for containers you trust.
160 &quot;mounts&quot;: [ # A list of mounts to make available to the action.
161 #
162 # In addition to the values specified here, every action has a special
163 # virtual disk mounted under `/google` that contains log files and other
164 # operational components.
165 #
166 # &lt;ul&gt;
167 # &lt;li&gt;&lt;code&gt;/google/logs&lt;/code&gt; All logs written during the pipeline
168 # execution.&lt;/li&gt;
169 # &lt;li&gt;&lt;code&gt;/google/logs/output&lt;/code&gt; The combined standard output and
170 # standard error of all actions run as part of the pipeline
171 # execution.&lt;/li&gt;
172 # &lt;li&gt;&lt;code&gt;/google/logs/action/*/stdout&lt;/code&gt; The complete contents of
173 # each individual action&#x27;s standard output.&lt;/li&gt;
174 # &lt;li&gt;&lt;code&gt;/google/logs/action/*/stderr&lt;/code&gt; The complete contents of
175 # each individual action&#x27;s standard error output.&lt;/li&gt;
176 # &lt;/ul&gt;
177 { # Carries information about a particular disk mount inside a container.
178 &quot;path&quot;: &quot;A String&quot;, # The path to mount the disk inside the container.
179 &quot;disk&quot;: &quot;A String&quot;, # The name of the disk to mount, as specified in the resources section.
180 &quot;readOnly&quot;: True or False, # If true, the disk is mounted read-only inside the container.
181 },
182 ],
183 &quot;alwaysRun&quot;: True or False, # By default, after an action fails, no further actions are run. This flag
184 # indicates that this action must be run even if the pipeline has already
185 # failed. This is useful for actions that copy output files off of the VM
186 # or for debugging. Note that no actions will be run if image prefetching
187 # fails.
188 &quot;credentials&quot;: { # Holds encrypted information that is only decrypted and stored in RAM # If the specified image is hosted on a private registry other than Google
189 # Container Registry, the credentials required to pull the image must be
190 # specified here as an encrypted secret.
191 #
192 # The secret must decrypt to a JSON-encoded dictionary containing both
193 # `username` and `password` keys.
194 # by the worker VM when running the pipeline.
195 &quot;cipherText&quot;: &quot;A String&quot;, # The value of the cipherText response from the `encrypt` method. This field
196 # is intentionally unaudited.
197 &quot;keyName&quot;: &quot;A String&quot;, # The name of the Cloud KMS key that will be used to decrypt the secret
198 # value. The VM service account must have the required permissions and
199 # authentication scopes to invoke the `decrypt` method on the specified key.
200 },
201 &quot;pidNamespace&quot;: &quot;A String&quot;, # An optional identifier for a PID namespace to run the action inside.
202 # Multiple actions should use the same string to share a namespace. If
203 # unspecified, a separate isolated namespace is used.
204 &quot;imageUri&quot;: &quot;A String&quot;, # Required. The URI to pull the container image from. Note that all images referenced
205 # by actions in the pipeline are pulled before the first action runs. If
206 # multiple actions reference the same image, it is only pulled once,
207 # ensuring that the same image is used for all actions in a single pipeline.
208 #
209 # The image URI can be either a complete host and image specification (e.g.,
210 # quay.io/biocontainers/samtools), a library and image name (e.g.,
211 # google/cloud-sdk) or a bare image name (&#x27;bash&#x27;) to pull from the default
212 # library. No schema is required in any of these cases.
213 #
214 # If the specified image is not public, the service account specified for
215 # the Virtual Machine must have access to pull the images from GCR, or
216 # appropriate credentials must be specified in the
217 # google.cloud.lifesciences.v2beta.Action.credentials field.
218 &quot;disableStandardErrorCapture&quot;: True or False, # A small portion of the container&#x27;s standard error stream is typically
219 # captured and returned inside the `ContainerStoppedEvent`. Setting this
220 # flag disables this functionality.
221 &quot;entrypoint&quot;: &quot;A String&quot;, # If specified, overrides the `ENTRYPOINT` specified in the container.
222 &quot;portMappings&quot;: { # A map of containers to host port mappings for this container. If the
223 # container already specifies exposed ports, use the
224 # `PUBLISH_EXPOSED_PORTS` flag instead.
225 #
226 # The host port number must be less than 65536. If it is zero, an unused
227 # random port is assigned. To determine the resulting port number, consult
228 # the `ContainerStartedEvent` in the operation metadata.
229 &quot;a_key&quot;: 42,
230 },
231 &quot;disableImagePrefetch&quot;: True or False, # All container images are typically downloaded before any actions are
232 # executed. This helps prevent typos in URIs or issues like lack of disk
233 # space from wasting large amounts of compute resources.
234 #
235 # If set, this flag prevents the worker from downloading the image until
236 # just before the action is executed.
237 &quot;timeout&quot;: &quot;A String&quot;, # The maximum amount of time to give the action to complete. If the action
238 # fails to complete before the timeout, it will be terminated and the exit
239 # status will be non-zero. The pipeline will continue or terminate based
240 # on the rules defined by the `ALWAYS_RUN` and `IGNORE_EXIT_STATUS` flags.
241 &quot;ignoreExitStatus&quot;: True or False, # Normally, a non-zero exit status causes the pipeline to fail. This flag
242 # allows execution of other actions to continue instead.
243 &quot;runInBackground&quot;: True or False, # This flag allows an action to continue running in the background while
244 # executing subsequent actions. This is useful to provide services to
245 # other actions (or to provide debugging support tools like SSH servers).
246 },
247 ],
Bu Sun Kim65020912020-05-20 12:08:20 -0700248 &quot;timeout&quot;: &quot;A String&quot;, # The maximum amount of time to give the pipeline to complete. This includes
249 # the time spent waiting for a worker to be allocated. If the pipeline fails
250 # to complete before the timeout, it will be cancelled and the error code
251 # will be set to DEADLINE_EXCEEDED.
252 #
253 # If unspecified, it will default to 7 days.
254 &quot;resources&quot;: { # The system resources for the pipeline run. # The resources required for execution.
255 #
256 # At least one zone or region must be specified or the pipeline run will fail.
Bu Sun Kim4ed7d3f2020-05-27 12:20:54 -0700257 &quot;zones&quot;: [ # The list of zones allowed for VM allocation. If set, the `regions` field
258 # must not be set.
259 &quot;A String&quot;,
260 ],
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700261 &quot;regions&quot;: [ # The list of regions allowed for VM allocation. If set, the `zones` field
262 # must not be set.
263 &quot;A String&quot;,
264 ],
Bu Sun Kim65020912020-05-20 12:08:20 -0700265 &quot;virtualMachine&quot;: { # Carries information about a Compute Engine VM resource. # The virtual machine specification.
Bu Sun Kim65020912020-05-20 12:08:20 -0700266 &quot;bootDiskSizeGb&quot;: 42, # The size of the boot disk, in GB. The boot disk must be large
267 # enough to accommodate all of the Docker images from each action in the
268 # pipeline at the same time. If not specified, a small but reasonable
269 # default value is used.
Bu Sun Kim65020912020-05-20 12:08:20 -0700270 &quot;accelerators&quot;: [ # The list of accelerators to attach to the VM.
271 { # Carries information about an accelerator that can be attached to a VM.
272 &quot;count&quot;: &quot;A String&quot;, # How many accelerators of this type to attach.
273 &quot;type&quot;: &quot;A String&quot;, # The accelerator type string (for example, &quot;nvidia-tesla-k80&quot;).
274 #
275 # Only NVIDIA GPU accelerators are currently supported. If an NVIDIA GPU is
276 # attached, the required runtime libraries will be made available to all
277 # containers under `/usr/local/nvidia`. The driver version to install must
278 # be specified using the NVIDIA driver version parameter on the virtual
279 # machine specification. Note that attaching a GPU increases the worker VM
280 # startup time by a few minutes.
281 },
282 ],
283 &quot;machineType&quot;: &quot;A String&quot;, # Required. The machine type of the virtual machine to create. Must be the short name
284 # of a standard machine type (such as &quot;n1-standard-1&quot;) or a custom machine
285 # type (such as &quot;custom-1-4096&quot;, where &quot;1&quot; indicates the number of vCPUs and
286 # &quot;4096&quot; indicates the memory in MB). See
287 # [Creating an instance with a custom machine
288 # type](https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type#create)
289 # for more specifications on creating a custom machine type.
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700290 &quot;labels&quot;: { # Optional set of labels to apply to the VM and any attached disk resources.
291 # These labels must adhere to the [name and value
292 # restrictions](https://cloud.google.com/compute/docs/labeling-resources) on
293 # VM labels imposed by Compute Engine.
Bu Sun Kim65020912020-05-20 12:08:20 -0700294 #
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700295 # Labels keys with the prefix &#x27;google-&#x27; are reserved for use by Google.
296 #
297 # Labels applied at creation time to the VM. Applied on a best-effort basis
298 # to attached disk resources shortly after VM creation.
299 &quot;a_key&quot;: &quot;A String&quot;,
Bu Sun Kim65020912020-05-20 12:08:20 -0700300 },
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700301 &quot;dockerCacheImages&quot;: [ # The Compute Engine Disk Images to use as a Docker cache. The disks will be
302 # mounted into the Docker folder in a way that the images present in the
303 # cache will not need to be pulled. The digests of the cached images must
304 # match those of the tags used or the latest version will still be pulled.
305 # Only a single image is supported.
Bu Sun Kim65020912020-05-20 12:08:20 -0700306 &quot;A String&quot;,
307 ],
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700308 &quot;enableStackdriverMonitoring&quot;: True or False, # Whether Stackdriver monitoring should be enabled on the VM.
309 &quot;bootImage&quot;: &quot;A String&quot;, # The host operating system image to use.
Bu Sun Kim65020912020-05-20 12:08:20 -0700310 #
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700311 # Currently, only Container-Optimized OS images can be used.
Bu Sun Kim65020912020-05-20 12:08:20 -0700312 #
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700313 # The default value is `projects/cos-cloud/global/images/family/cos-stable`,
314 # which selects the latest stable release of Container-Optimized OS.
Bu Sun Kim65020912020-05-20 12:08:20 -0700315 #
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700316 # This option is provided to allow testing against the beta release of the
317 # operating system to ensure that the new version does not interact
318 # negatively with production pipelines.
Bu Sun Kim65020912020-05-20 12:08:20 -0700319 #
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700320 # To test a pipeline against the beta release of Container-Optimized OS,
321 # use the value `projects/cos-cloud/global/images/family/cos-beta`.
322 &quot;cpuPlatform&quot;: &quot;A String&quot;, # The CPU platform to request. An instance based on a newer platform can be
323 # allocated, but never one with fewer capabilities. The value of this
324 # parameter must be a valid Compute Engine CPU platform name (such as &quot;Intel
325 # Skylake&quot;). This parameter is only useful for carefully optimized work
326 # loads where the CPU platform has a significant impact.
Bu Sun Kim65020912020-05-20 12:08:20 -0700327 #
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700328 # For more information about the effect of this parameter, see
329 # https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform.
330 &quot;preemptible&quot;: True or False, # If true, allocate a preemptible VM.
331 &quot;disks&quot;: [ # The list of disks to create and attach to the VM.
332 { # Carries information about a disk that can be attached to a VM.
333 #
334 # See https://cloud.google.com/compute/docs/disks/performance for more
335 # information about disk type, size, and performance considerations.
336 &quot;type&quot;: &quot;A String&quot;, # The Compute Engine disk type. If unspecified, `pd-standard` is used.
337 &quot;sizeGb&quot;: 42, # The size, in GB, of the disk to attach. If the size is not
338 # specified, a default is chosen to ensure reasonable I/O performance.
339 #
340 # If the disk type is specified as `local-ssd`, multiple local drives are
341 # automatically combined to provide the requested size. Note, however, that
342 # each physical SSD is 375GB in size, and no more than 8 drives can be
343 # attached to a single instance.
344 &quot;sourceImage&quot;: &quot;A String&quot;, # An optional image to put on the disk before attaching it to the VM.
345 &quot;name&quot;: &quot;A String&quot;, # A user-supplied name for the disk. Used when mounting the disk into
346 # actions. The name must contain only upper and lowercase alphanumeric
347 # characters and hyphens and cannot start with a hyphen.
Bu Sun Kim4ed7d3f2020-05-27 12:20:54 -0700348 },
349 ],
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700350 &quot;nvidiaDriverVersion&quot;: &quot;A String&quot;, # The NVIDIA driver version to use when attaching an NVIDIA GPU accelerator.
351 # The version specified here must be compatible with the GPU libraries
352 # contained in the container being executed, and must be one of the drivers
353 # hosted in the `nvidia-drivers-us-public` bucket on Google Cloud Storage.
354 &quot;serviceAccount&quot;: { # Carries information about a Google Cloud service account. # The service account to install on the VM. This account does not need
355 # any permissions other than those required by the pipeline.
356 &quot;scopes&quot;: [ # List of scopes to be enabled for this service account on the VM, in
357 # addition to the cloud-platform API scope that will be added by default.
358 &quot;A String&quot;,
359 ],
360 &quot;email&quot;: &quot;A String&quot;, # Email address of the service account. If not specified, the default
361 # Compute Engine service account for the project will be used.
362 },
363 &quot;network&quot;: { # VM networking options. # The VM network configuration.
364 &quot;network&quot;: &quot;A String&quot;, # The network name to attach the VM&#x27;s network interface to. The value will
365 # be prefixed with `global/networks/` unless it contains a `/`, in which
366 # case it is assumed to be a fully specified network resource URL.
367 #
368 # If unspecified, the global default network is used.
369 &quot;usePrivateAddress&quot;: True or False, # If set to true, do not attach a public IP address to the VM. Note that
370 # without a public IP address, additional configuration is required to
371 # allow the VM to access Google services.
372 #
373 # See https://cloud.google.com/vpc/docs/configure-private-google-access
374 # for more information.
375 &quot;subnetwork&quot;: &quot;A String&quot;, # If the specified network is configured for custom subnet creation, the
376 # name of the subnetwork to attach the instance to must be specified here.
377 #
378 # The value is prefixed with `regions/*/subnetworks/` unless it contains a
379 # `/`, in which case it is assumed to be a fully specified subnetwork
380 # resource URL.
381 #
382 # If the `*` character appears in the value, it is replaced with the region
383 # that the virtual machine has been allocated in.
384 },
Bu Sun Kim65020912020-05-20 12:08:20 -0700385 },
Bu Sun Kim4ed7d3f2020-05-27 12:20:54 -0700386 },
387 },
388 &quot;labels&quot;: { # User-defined labels to associate with the returned operation. These
389 # labels are not propagated to any Google Cloud Platform resources used by
390 # the operation, and can be modified at any time.
391 #
392 # To associate labels with resources created while executing the operation,
393 # see the appropriate resource message (for example, `VirtualMachine`).
394 &quot;a_key&quot;: &quot;A String&quot;,
Bu Sun Kim65020912020-05-20 12:08:20 -0700395 },
396 }
397
398 x__xgafv: string, V1 error format.
399 Allowed values
400 1 - v1 error format
401 2 - v2 error format
402
403Returns:
404 An object of the form:
405
406 { # This resource represents a long-running operation that is the result of a
407 # network API call.
408 &quot;response&quot;: { # An Empty object.
409 &quot;a_key&quot;: &quot;&quot;, # Properties of the object. Contains field @type with type URL.
410 },
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700411 &quot;done&quot;: True or False, # If the value is `false`, it means the operation is still in progress.
412 # If `true`, the operation is completed, and either `error` or `response` is
413 # available.
Bu Sun Kim65020912020-05-20 12:08:20 -0700414 &quot;error&quot;: { # The `Status` type defines a logical error model that is suitable for # The error result of the operation in case of failure or cancellation.
415 # different programming environments, including REST APIs and RPC APIs. It is
416 # used by [gRPC](https://github.com/grpc). Each `Status` message contains
417 # three pieces of data: error code, error message, and error details.
418 #
419 # You can find out more about this error model and how to work with it in the
420 # [API Design Guide](https://cloud.google.com/apis/design/errors).
Bu Sun Kim65020912020-05-20 12:08:20 -0700421 &quot;details&quot;: [ # A list of messages that carry the error details. There is a common set of
422 # message types for APIs to use.
423 {
424 &quot;a_key&quot;: &quot;&quot;, # Properties of the object. Contains field @type with type URL.
425 },
426 ],
427 &quot;code&quot;: 42, # The status code, which should be an enum value of google.rpc.Code.
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700428 &quot;message&quot;: &quot;A String&quot;, # A developer-facing error message, which should be in English. Any
429 # user-facing error message should be localized and sent in the
430 # google.rpc.Status.details field, or localized by the client.
Bu Sun Kim65020912020-05-20 12:08:20 -0700431 },
432 &quot;metadata&quot;: { # An Metadata object. This will always be returned with the Operation.
433 &quot;a_key&quot;: &quot;&quot;, # Properties of the object. Contains field @type with type URL.
434 },
Bu Sun Kimd059ad82020-07-22 17:02:09 -0700435 &quot;name&quot;: &quot;A String&quot;, # The server-assigned name for the operation. This may be passed to the other operation methods to retrieve information about the operation&#x27;s status.
Bu Sun Kim65020912020-05-20 12:08:20 -0700436 }</pre>
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