feat: Add new gcloud commands, API clients, and third-party libraries across various services.

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/__init__.py

@@ -0,0 +1,33 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2019 Google LLC. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""The command group for the Cloud Life Sciences CLI."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.calliope import base
+
+
+@base.ReleaseTracks(base.ReleaseTrack.ALPHA, base.ReleaseTrack.BETA)
+class Lifesciences(base.Group):
+  """Manage Cloud Life Sciences resources."""
+  category = base.SOLUTIONS_CATEGORY
+
+  def Filter(self, context, args):
+    # TODO(b/190534871):  Determine if command group works with project number
+    base.RequireProjectID(args)
+    del context, args

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/locations/__init__.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2020 Google LLC. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""The locations command group for the Cloud Life Sciences API CLI."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.calliope import base
+
+
+@base.ReleaseTracks(base.ReleaseTrack.ALPHA, base.ReleaseTrack.BETA)
+class Locations(base.Group):
+  """Query Cloud Life Sciences locations."""

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/locations/describe.yaml

@@ -0,0 +1,16 @@
+- help_text:
+    brief:  Describe a Cloud Life Sciences location.
+    description: Describe a Cloud Life Sciences location.
+    examples: |
+      To describe a location (for example, us-central1) called `my-location`, run:
+
+        $ {command} my-location
+
+  request:
+    collection: lifesciences.projects.locations
+    api_version: v2beta
+
+  arguments:
+    resource:
+      help_text: Cloud Life Sciences location to describe.
+      spec: !REF googlecloudsdk.command_lib.lifesciences.resources:location

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/locations/list.yaml

@@ -0,0 +1,25 @@
+- help_text:
+    brief:  List all locations where Cloud Life Sciences is available.
+    description: List all locations where Cloud Life Sciences is available.
+    examples: |
+      To list all locations, run:
+
+        $ {command}
+
+  request:
+    collection: lifesciences.projects.locations
+    api_version: v2beta
+
+  response:
+    id_field: name
+
+  arguments:
+    resource:
+      help_text: The parent project of Cloud Life Sciences Locations to list.
+      spec: !REF googlecloudsdk.command_lib.lifesciences.resources:project
+
+  output:
+    format: |
+      table(
+        name
+      )

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/operations/__init__.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2019 Google LLC. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""The operations command group for the Cloud Life Sciences API CLI."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.calliope import base
+
+
+@base.ReleaseTracks(base.ReleaseTrack.ALPHA, base.ReleaseTrack.BETA)
+class Operations(base.Group):
+  """Manage Cloud Life Sciences operations."""

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/operations/cancel.yaml

@@ -0,0 +1,21 @@
+- help_text:
+    brief: Cancel a Cloud Life Sciences operation.
+    description: Cancel a Cloud Life Sciences operation.
+    examples: |
+      To cancel an operation called `my-operation`, run:
+
+        $ {command} my-operation
+
+  request:
+    collection: lifesciences.projects.locations.operations
+    api_version: v2beta
+    method: cancel
+
+  arguments:
+    resource:
+      help_text: Cloud Life Sciences operation to cancel.
+      spec: !REF googlecloudsdk.command_lib.lifesciences.resources:operation
+
+  input:
+    confirmation_prompt: |
+      Operation [{__name__}] will be canceled.

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/operations/describe.yaml

@@ -0,0 +1,16 @@
+- help_text:
+    brief:  Describe a Cloud Life Sciences operation.
+    description: Describe a Cloud Life Sciences operation.
+    examples: |
+      To describe an operation called `my-operation`, run:
+
+        $ {command} my-operation
+
+  request:
+    collection: lifesciences.projects.locations.operations
+    api_version: v2beta
+
+  arguments:
+    resource:
+      help_text: Cloud Life Sciences operation to describe.
+      spec: !REF googlecloudsdk.command_lib.lifesciences.resources:operation

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/operations/list.yaml

@@ -0,0 +1,27 @@
+- help_text:
+    brief:  List Cloud Life Sciences operations.
+    description: List Cloud Life Sciences operations.
+    examples: |
+      To list all operations, run:
+
+        $ {command}
+
+  request:
+    collection: lifesciences.projects.locations.operations
+    api_version: v2beta
+
+  response:
+    id_field: name
+
+  arguments:
+    resource:
+      help_text: Cloud Life Sciences Location of the Operations to list.
+      spec: !REF googlecloudsdk.command_lib.lifesciences.resources:location
+
+  output:
+    format: |
+      table(
+          name.scope("operations"):label=ID,
+          name.scope("locations").segment(0):label=LOCATION,
+          done:label=DONE
+      )

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/operations/wait.py

@@ -0,0 +1,63 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2019 Google Inc. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Command to wait for Cloud Life Sciences operation to complete."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.api_lib.lifesciences import lifesciences_client
+from googlecloudsdk.api_lib.util import waiter
+from googlecloudsdk.calliope import base
+from googlecloudsdk.calliope.concepts import concepts
+from googlecloudsdk.command_lib.lifesciences import operation_poller
+from googlecloudsdk.command_lib.util.apis import yaml_data
+from googlecloudsdk.command_lib.util.concepts import concept_parsers
+
+
+class Wait(base.SilentCommand):
+  r"""Wait for Cloud Life Sciences operation to complete.
+
+  ## EXAMPLES
+  To wait for the completion of the operation called `my-operation`, run:
+
+    $ {command} my-operation
+  """
+
+  WAIT_CEILING_MS = 60 * 20 * 1000
+
+  @staticmethod
+  def Args(parser):
+    operation_spec = concepts.ResourceSpec.FromYaml(
+        yaml_data.ResourceYAMLData.FromPath('lifesciences.operation')
+        .GetData())
+    concept_parsers.ConceptParser.ForResource(
+        'operation', operation_spec, 'The Cloud Life Sciences operation to wait for.',
+        required=True).AddToParser(parser)
+
+  def Run(self, args):
+    client = lifesciences_client.LifeSciencesClient()
+    operation_ref = args.CONCEPTS.operation.Parse()
+
+    req = client.messages.LifesciencesProjectsLocationsOperationsGetRequest(
+        name=operation_ref.RelativeName())
+
+    operation = client.client.projects_locations_operations.Get(req)
+
+    waiter.WaitFor(
+        operation_poller.OperationPoller(),
+        operation.name,
+        'Waiting for [{}] to complete.'.format(operation.name),
+        wait_ceiling_ms=self.WAIT_CEILING_MS)

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/pipelines/__init__.py

@@ -0,0 +1,49 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2019 Google LLC. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Life Sciences pipelines sub-group."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.api_lib import lifesciences as lib
+from googlecloudsdk.api_lib.util import apis
+from googlecloudsdk.calliope import base
+
+
+@base.ReleaseTracks(base.ReleaseTrack.ALPHA, base.ReleaseTrack.BETA)
+class Workflows(base.Group):
+  """Commands for Life Sciences pipelines.
+
+  Command to run pipelines.
+  """
+
+  def Filter(self, context, args):
+    """Setup the API client within the context for this group's commands.
+
+    Args:
+      context: {str:object}, A set of key-value pairs that can be used for
+          common initialization among commands.
+      args: argparse.Namespace: The same namespace given to the corresponding
+          .Run() invocation.
+
+    Returns:
+      The updated context.
+    """
+
+    context[lib.STORAGE_V1_CLIENT_KEY] = apis.GetClientInstance(
+        'storage', 'v1')
+    return context

gcloud auth application-default login/google-cloud-sdk/lib/surface/lifesciences/pipelines/run.py

@@ -0,0 +1,484 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2019 Google LLC. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Implementation of gcloud lifesciences pipelines run.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+import base64
+from googlecloudsdk.api_lib import lifesciences as lib
+from googlecloudsdk.api_lib.lifesciences import exceptions
+from googlecloudsdk.api_lib.lifesciences import lifesciences_util
+from googlecloudsdk.calliope import arg_parsers
+from googlecloudsdk.calliope import base
+from googlecloudsdk.calliope.concepts import concepts
+from googlecloudsdk.command_lib.util.apis import yaml_data
+from googlecloudsdk.command_lib.util.args import labels_util
+from googlecloudsdk.command_lib.util.concepts import concept_parsers
+from googlecloudsdk.core import log
+from googlecloudsdk.core import properties
+from googlecloudsdk.core.util import files
+import six
+
+CLOUD_SDK_IMAGE = 'google/cloud-sdk:slim'
+SHARED_DISK = 'gcloud-shared'
+
+
+class _SharedPathGenerator(object):
+
+  def __init__(self, root):
+    self.root = root
+    self.index = -1
+
+  def Generate(self):
+    self.index += 1
+    return '/%s/%s%d' % (SHARED_DISK, self.root, self.index)
+
+
+def _ValidateAndMergeArgInputs(args):
+  """Turn args.inputs and args.inputs_from_file dicts into a single dict.
+
+  Args:
+    args: The parsed command-line arguments
+
+  Returns:
+    A dict that is the merge of args.inputs and args.inputs_from_file
+  Raises:
+    files.Error
+  """
+
+  is_local_file = {}
+
+  # If no inputs from file, then no validation or merge needed
+  if not args.inputs_from_file:
+    return args.inputs, is_local_file
+
+  # Initialize the merged dictionary
+  arg_inputs = {}
+
+  if args.inputs:
+    # Validate args.inputs and args.inputs-from-file do not overlap
+    overlap = set(args.inputs.keys()).intersection(
+        set(args.inputs_from_file.keys()))
+    if overlap:
+      raise exceptions.LifeSciencesError(
+          '--{0} and --{1} may not specify overlapping values: {2}'
+          .format('inputs', 'inputs-from-file', ', '.join(overlap)))
+
+    # Add the args.inputs
+    arg_inputs.update(args.inputs)
+
+  # Read up the inputs-from-file and add the values from the file
+  for key, value in six.iteritems(args.inputs_from_file):
+    arg_inputs[key] = files.ReadFileContents(value)
+    is_local_file[key] = True
+
+  return arg_inputs, is_local_file
+
+
+class Run(base.SilentCommand):
+  r"""Defines and runs a pipeline.
+
+  A pipeline is a transformation of a set of inputs to a set of outputs.
+  Supports Docker-based commands.
+
+  ## EXAMPLES
+  To run a pipeline described in the `pipeline.json` file, run:
+
+    $ {command} --pipeline-file=pipeline.json
+  """
+
+  @staticmethod
+  def Args(parser):
+    """Args is called by calliope to gather arguments for this command.
+
+    Args:
+      parser: An argparse parser that you can use to add arguments that go
+          on the command line after this command. Positional arguments are
+          allowed.
+    """
+    location_spec = concepts.ResourceSpec.FromYaml(
+        yaml_data.ResourceYAMLData.FromPath('lifesciences.location')
+        .GetData())
+    concept_parsers.ConceptParser.ForResource(
+        '--location',
+        location_spec,
+        'The Google Cloud location to run the pipeline.',
+        required=True).AddToParser(parser)
+
+    pipeline = parser.add_mutually_exclusive_group(required=True)
+    pipeline.add_argument(
+        '--pipeline-file',
+        help='''A YAML or JSON file containing a Pipeline object. See
+[](https://cloud.google.com/life-sciences/docs/reference/rest/v2beta/projects.locations.pipelines/run#pipeline)
+''')
+    pipeline.add_argument(
+        '--command-line',
+        category=base.COMMONLY_USED_FLAGS,
+        help='''Command line to run with /bin/sh in the specified
+            Docker image. Cannot be used with --pipeline-file.''')
+
+    parser.add_argument(
+        '--docker-image',
+        category=base.COMMONLY_USED_FLAGS,
+        default=CLOUD_SDK_IMAGE,
+        help='''A Docker image to run. Requires --command-line to
+            be specified and cannot be used with --pipeline-file.''')
+
+    parser.add_argument(
+        '--inputs',
+        category=base.COMMONLY_USED_FLAGS,
+        metavar='NAME=VALUE',
+        type=arg_parsers.ArgDict(),
+        action=arg_parsers.UpdateAction,
+        help='''Map of input PipelineParameter names to values.
+            Used to pass literal parameters to the pipeline, and to specify
+            input files in Google Cloud Storage that will have a localCopy
+            made. Specified as a comma-separated list: --inputs
+            file=gs://my-bucket/in.txt,name=hello''')
+
+    parser.add_argument(
+        '--inputs-from-file',
+        category=base.COMMONLY_USED_FLAGS,
+        metavar='NAME=FILE',
+        type=arg_parsers.ArgDict(),
+        action=arg_parsers.UpdateAction,
+        help='''Map of input PipelineParameter names to values.
+            Used to pass literal parameters to the pipeline where values come
+            from local files; this can be used to send large pipeline input
+            parameters, such as code, data, or configuration values.
+            Specified as a comma-separated list:
+            --inputs-from-file script=myshellscript.sh,pyfile=mypython.py''')
+
+    parser.add_argument(
+        '--outputs',
+        category=base.COMMONLY_USED_FLAGS,
+        metavar='NAME=VALUE',
+        type=arg_parsers.ArgDict(),
+        action=arg_parsers.UpdateAction,
+        help='''Map of output PipelineParameter names to values.
+            Used to specify output files in Google Cloud Storage that will be
+            made from a localCopy. Specified as a comma-separated list:
+            --outputs ref=gs://my-bucket/foo,ref2=gs://my-bucket/bar''')
+
+    parser.add_argument(
+        '--logging',
+        category=base.COMMONLY_USED_FLAGS,
+        help='''The location in Google Cloud Storage to which the pipeline logs
+            will be copied. Can be specified as a fully qualified directory
+            path, in which case logs will be output with a unique identifier
+            as the filename in that directory, or as a fully specified path,
+            which must end in `.log`, in which case that path will be
+            used. Stdout and stderr logs from the run are also generated and
+            output as `-stdout.log` and `-stderr.log`.''')
+
+    parser.add_argument(
+        '--env-vars',
+        category=base.COMMONLY_USED_FLAGS,
+        metavar='NAME=VALUE',
+        type=arg_parsers.ArgDict(),
+        help='''List of key-value pairs to set as environment variables.''')
+
+    labels_util.AddCreateLabelsFlags(parser)
+
+    parser.add_argument(
+        '--disk-size',
+        category=base.COMMONLY_USED_FLAGS,
+        default=None,
+        help='''The disk size(s) in GB, specified as a comma-separated list of
+            pairs of disk name and size. For example:
+            --disk-size "name:size,name2:size2".
+            Overrides any values specified in the pipeline-file.''')
+
+    parser.add_argument(
+        '--preemptible',
+        category=base.COMMONLY_USED_FLAGS,
+        action='store_true',
+        help='''Whether to use a preemptible VM for this pipeline. The
+            "resource" section of the pipeline-file must also set preemptible
+            to "true" for this flag to take effect.''')
+
+    parser.add_argument(
+        '--run-id',
+        hidden=True,
+        help='THIS ARGUMENT NEEDS HELP TEXT.')
+
+    parser.add_argument(
+        '--service-account-email',
+        default='default',
+        help='''The service account used on the Compute Engine VMs that run the
+            pipeline. If unspecified, defaults to the Compute Engine service
+            account for your project.''')
+
+    parser.add_argument(
+        '--service-account-scopes',
+        metavar='SCOPE',
+        type=arg_parsers.ArgList(),
+        default=[],
+        help='''List of additional scopes to be made available for this service
+             account. The following scopes are always requested:
+
+             https://www.googleapis.com/auth/cloud-platform''')
+
+    parser.add_argument(
+        '--machine-type',
+        default='n1-standard-1',
+        help='''The type of VirtualMachine to use. Defaults to n1-standard-1.''')
+
+    parser.add_argument(
+        '--zones',
+        metavar='ZONE',
+        type=arg_parsers.ArgList(),
+        help='''List of Compute Engine zones the pipeline can run in.
+
+If no zones are specified with the zones flag, then zones in the
+pipeline definition file will be used.
+
+If no zones are specified in the pipeline definition, then the
+default zone in your local client configuration is used (and must be specified).
+
+For more information on default zones, see
+https://cloud.google.com/compute/docs/gcloud-compute/#set_default_zone_and_region_in_your_local_client''')
+
+    parser.add_argument(
+        '--regions',
+        metavar='REGION',
+        type=arg_parsers.ArgList(),
+        help='''List of Compute Engine regions the pipeline can
+            run in.
+
+If no regions are specified with the regions flag, then regions in the
+pipeline definition file will be used.
+
+If no regions are specified in the pipeline definition, then the
+default region in your local client configuration is used.
+
+At least one region or region must be specified.
+
+For more information on default regions, see
+https://cloud.google.com/compute/docs/gcloud-compute/#set_default_zone_and_region_in_your_local_client''')
+
+    parser.add_argument(
+        '--network',
+        help='''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.''')
+
+    parser.add_argument(
+        '--subnetwork',
+        help='''The subnetwork to use on the provided network.
+
+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.''')
+
+    parser.add_argument(
+        '--boot-disk-size',
+        type=int,
+        help='''The size of the boot disk in GB.
+
+The boot disk size must be large enough to accommodate all Docker images from
+each action in the pipeline at the same time. If not specified, a small but
+reasonable default value is used.''')
+
+  def Run(self, args):
+    """This is what gets called when the user runs this command.
+
+    Args:
+      args: argparse.Namespace, All the arguments that were provided to this
+        command invocation.
+
+    Raises:
+      files.Error: A file argument could not be read.
+      LifeSciencesError: User input was invalid.
+      HttpException: An http error response was received while executing api
+          request.
+    Returns:
+      Operation representing the running pipeline.
+    """
+    pipeline = None
+    apitools_client = lifesciences_util.GetLifeSciencesClient('v2beta')
+    lifesciences_messages = lifesciences_util.GetLifeSciencesMessages('v2beta')
+    if args.pipeline_file:
+      pipeline = lifesciences_util.GetFileAsMessage(
+          args.pipeline_file,
+          lifesciences_messages.Pipeline,
+          self.context[lib.STORAGE_V1_CLIENT_KEY])
+    elif args.command_line:
+      pipeline = lifesciences_messages.Pipeline(
+          actions=[lifesciences_messages.Action(
+              imageUri=args.docker_image,
+              commands=['-c', args.command_line],
+              entrypoint='bash')])
+
+    arg_inputs, is_local_file = _ValidateAndMergeArgInputs(args)
+
+    request = None
+    # Create messages up front to avoid checking for None everywhere.
+    if not pipeline.resources:
+      pipeline.resources = lifesciences_messages.Resources()
+    resources = pipeline.resources
+
+    if not resources.virtualMachine:
+      resources.virtualMachine = lifesciences_messages.VirtualMachine(
+          machineType=args.machine_type)
+    virtual_machine = resources.virtualMachine
+
+    if not virtual_machine.serviceAccount:
+      virtual_machine.serviceAccount = lifesciences_messages.ServiceAccount()
+
+    if args.preemptible:
+      virtual_machine.preemptible = args.preemptible
+
+    if args.zones:
+      resources.zones = args.zones
+    elif not resources.zones and properties.VALUES.compute.zone.Get():
+      resources.zones = [properties.VALUES.compute.zone.Get()]
+
+    if args.regions:
+      resources.regions = args.regions
+    elif not resources.regions and properties.VALUES.compute.region.Get():
+      resources.regions = [properties.VALUES.compute.region.Get()]
+
+    if args.service_account_email != 'default':
+      virtual_machine.serviceAccount.email = args.service_account_email
+
+    if args.service_account_scopes:
+      virtual_machine.serviceAccount.scopes = args.service_account_scopes
+
+    # Always add the cloud-platform scope for user convenience.
+    virtual_machine.serviceAccount.scopes.append(
+        'https://www.googleapis.com/auth/cloud-platform')
+
+    # Attach custom network/subnetwork (if set).
+    if args.network or args.subnetwork:
+      if not virtual_machine.network:
+        virtual_machine.network = lifesciences_messages.Network()
+      if args.network:
+        virtual_machine.network.network = args.network
+      if args.subnetwork:
+        virtual_machine.network.subnetwork = args.subnetwork
+
+    if args.boot_disk_size is not None:
+      if args.boot_disk_size <= 0:
+        raise exceptions.LifeSciencesError(
+            'Boot disk size must be greater than zero.')
+      virtual_machine.bootDiskSizeGb = args.boot_disk_size
+
+    # Generate paths for inputs and outputs in a shared location and put them
+    # into the environment for actions based on their name.
+    env = {}
+    if arg_inputs:
+      input_generator = _SharedPathGenerator('input')
+      for name, value in arg_inputs.items():
+        if lifesciences_util.IsGcsPath(value):
+          env[name] = input_generator.Generate()
+          pipeline.actions.insert(0, lifesciences_messages.Action(
+              imageUri=CLOUD_SDK_IMAGE,
+              commands=['/bin/sh', '-c', 'gsutil -m -q cp %s ${%s}' %
+                        (value, name)]))
+        elif name in is_local_file:
+          env[name] = input_generator.Generate()
+          pipeline.actions.insert(
+              0,
+              lifesciences_messages.Action(
+                  imageUri=CLOUD_SDK_IMAGE,
+                  commands=[
+                      '/bin/sh', '-c',
+                      'echo "%s" | base64 -d > ${%s}' %
+                      (base64.b64encode(value.encode()).decode(), name)
+                  ]))
+        else:
+          env[name] = value
+
+    if args.outputs:
+      output_generator = _SharedPathGenerator('output')
+      for name, value in args.outputs.items():
+        env[name] = output_generator.Generate()
+        pipeline.actions.append(lifesciences_messages.Action(
+            imageUri=CLOUD_SDK_IMAGE,
+            commands=['/bin/sh', '-c', 'gsutil -m -q cp ${%s} %s' % (name,
+                                                                       value)]))
+    if args.env_vars:
+      for name, value in args.env_vars.items():
+        env[name] = value
+
+    # Merge any existing pipeline arguments into the generated environment and
+    # update the pipeline.
+    if pipeline.environment:
+      for val in pipeline.environment.additionalProperties:
+        if val.key not in env:
+          env[val.key] = val.value
+
+    pipeline.environment = lifesciences_messages.Pipeline.EnvironmentValue(
+        additionalProperties=lifesciences_util.ArgDictToAdditionalPropertiesList(
+            env,
+            lifesciences_messages.Pipeline.EnvironmentValue.AdditionalProperty))
+
+    if arg_inputs or args.outputs:
+      virtual_machine.disks.append(lifesciences_messages.Disk(
+          name=SHARED_DISK))
+
+      for action in pipeline.actions:
+        action.mounts.append(lifesciences_messages.Mount(
+            disk=SHARED_DISK,
+            path='/' + SHARED_DISK))
+
+    if args.logging:
+      pipeline.actions.append(lifesciences_messages.Action(
+          imageUri=CLOUD_SDK_IMAGE,
+          commands=['/bin/sh', '-c',
+                    'gsutil -m -q cp /google/logs/output ' + args.logging],
+          alwaysRun=True))
+
+    # Update disk sizes if specified, potentially including the shared disk.
+    if args.disk_size:
+      disk_sizes = {}
+      for disk_encoding in args.disk_size.split(','):
+        parts = disk_encoding.split(':', 1)
+        try:
+          disk_sizes[parts[0]] = int(parts[1])
+        except:
+          raise exceptions.LifeSciencesError('Invalid --disk-size.')
+
+      for disk in virtual_machine.disks:
+        if disk.name in disk_sizes:
+          disk.sizeGb = disk_sizes[disk.name]
+
+    request = lifesciences_messages.RunPipelineRequest(
+        pipeline=pipeline,
+        labels=labels_util.ParseCreateArgs(
+            args, lifesciences_messages.RunPipelineRequest.LabelsValue))
+    projectId = lifesciences_util.GetProjectId()
+    location_ref = args.CONCEPTS.location.Parse()
+    request_wrapper = lifesciences_messages.LifesciencesProjectsLocationsPipelinesRunRequest(
+        parent=location_ref.RelativeName(),
+        runPipelineRequest=request)
+
+    result = apitools_client.projects_locations_pipelines.Run(request_wrapper)
+    log.status.Print('Running [{0}].'.format(result.name))
+    return result