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

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

@@ -0,0 +1,43 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2014 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 main command group for genomics.
+
+Everything under here will be the commands in your group.  Each file results in
+a command with that name.
+
+This module contains a single class that extends base.Group.  Calliope will
+dynamically search for the implementing class and use that as the command group
+for this command tree.  You can implement methods in this class to override some
+of the default behavior.
+"""
+
+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.DefaultUniverseOnly
+class Genomics(base.Group):
+  """Manage Genomics 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
+    base.DisableUserProjectQuota()

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

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2015 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.
+"""Genomics operations sub-group."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.calliope import base
+
+
+class Operations(base.Group):
+  """Commands for Genomics operations.
+
+  Commands to list, cancel, and examine operations.
+  """

gcloud auth application-default login/google-cloud-sdk/lib/surface/genomics/operations/cancel.py

@@ -0,0 +1,68 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2015 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 genomics operations cancel.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+import io
+
+from googlecloudsdk.api_lib.genomics import genomics_client
+from googlecloudsdk.api_lib.genomics.exceptions import GenomicsError
+from googlecloudsdk.calliope import base
+from googlecloudsdk.calliope import display
+from googlecloudsdk.command_lib.genomics import flags
+from googlecloudsdk.core import log
+from googlecloudsdk.core.console import console_io
+from googlecloudsdk.core.resource import resource_printer
+
+
+class Cancel(base.Command):
+  """Cancels an operation.
+  """
+
+  @staticmethod
+  def Args(parser):
+    """Register flags for this command."""
+    flags.AddName(parser)
+
+  def Run(self, args):
+    """This is what gets called when the user runs this command.
+
+    Args:
+      args: an argparse namespace, All the arguments that were provided to this
+        command invocation.
+
+    Raises:
+      HttpException: An http error response was received while executing api
+          request.
+    Returns:
+      None
+    """
+    client, resource = genomics_client.CreateFromName(args.name)
+    op = client.GetOperation(resource)
+
+    operation_string = io.StringIO()
+    print_format = display.Displayer(self, args).GetFormat()
+    resource_printer.Print(op, print_format, out=operation_string)
+
+    if not console_io.PromptContinue(message='%s\n%s' % (
+        operation_string.getvalue(), 'This operation will be canceled')):
+      raise GenomicsError('Cancel aborted by user.')
+
+    client.CancelOperation(resource)
+    log.status.write('Canceled [{0}].\n'.format(resource.RelativeName()))

gcloud auth application-default login/google-cloud-sdk/lib/surface/genomics/operations/describe.py

@@ -0,0 +1,47 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2015 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 genomics operations describe.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.api_lib.genomics import genomics_client
+from googlecloudsdk.calliope import base
+from googlecloudsdk.command_lib.genomics import flags
+
+
+class Describe(base.DescribeCommand):
+  """Returns details about an operation.
+  """
+
+  @staticmethod
+  def Args(parser):
+    """Register flags for this command."""
+    flags.AddName(parser)
+
+  def Run(self, args):
+    """This is what gets called when the user runs this command.
+
+    Args:
+      args: an argparse namespace, All the arguments that were provided to this
+        command invocation.
+
+    Returns:
+      a Operation message
+    """
+    client, resource = genomics_client.CreateFromName(args.name)
+    return client.GetOperation(resource)

gcloud auth application-default login/google-cloud-sdk/lib/surface/genomics/operations/list.py

@@ -0,0 +1,109 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2015 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 the gcloud genomics operations list command.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from apitools.base.py import list_pager
+
+from googlecloudsdk.api_lib.genomics import filter_rewrite
+from googlecloudsdk.api_lib.genomics import genomics_util
+from googlecloudsdk.calliope import base
+from googlecloudsdk.core import log
+
+
+class List(base.Command):
+  """List Genomics operations in a project.
+
+  Prints a table with summary information on operations in the project.
+  """
+
+  @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.
+    """
+    base.LIMIT_FLAG.AddToParser(parser)
+    parser.add_argument(
+        '--filter',
+        default='',
+        type=str,
+        help="""\
+        A string for filtering operations created with the v2alpha1 API. In
+        addition to typical operators (AND, OR, =, >, etc.) the following
+        filter fields are supported:
+
+          metadata.createTime - The time the operation was created as a
+                                timestamp YYYY-MM-DD HH:MM:SS<time zone>.  T can
+                                also be used as a separator between the date and
+                                time.  The time zone is optional and can be
+                                specified as an offset from UTC, a name, or 'Z'
+                                for UTC. Run $ gcloud topic datetimes
+                                to see more examples.
+                                    2018-02-15T16:53:38
+                                    2018-02-15 16:53:38-5:00
+                                    2018-02-15T16:53:38Z
+                                    2018-02-15 16:53:38 America/Los_Angeles
+                         done - A boolean for whether the operation has
+                                completed.
+                   error.code - A google.rpc.Code for a completed operation.
+              metadata.events - A set of strings for all events on the
+                                operation.
+                                    events:WorkerStartedEvent
+              metadata.labels - A map of string key and value for the operation.
+                                    labels.key = value
+                                    labels."key with space" = "value with space"
+                                For the existence of a key with any value.
+                                    labels.key:*
+        Run "$ gcloud topic filters" for more information.
+        """)
+
+  def Run(self, args):
+    """Run 'operations list'.
+
+    Args:
+      args: argparse.Namespace, The arguments that this command was invoked
+          with.
+
+    Returns:
+      The list of operations for this project.
+    """
+    apitools_client = genomics_util.GetGenomicsClient('v2alpha1')
+    genomics_messages = genomics_util.GetGenomicsMessages('v2alpha1')
+
+    request_filter = None
+    if args.filter:
+      rewriter = filter_rewrite.OperationsBackend()
+      args.filter, request_filter = rewriter.Rewrite(args.filter)
+      log.info('client_filter=%r server_filter=%r', args.filter, request_filter)
+
+    request = genomics_messages.GenomicsProjectsOperationsListRequest(
+        name='projects/%s/operations' % (genomics_util.GetProjectId(),),
+        filter=request_filter)
+
+    return list_pager.YieldFromList(
+        apitools_client.projects_operations,
+        request,
+        limit=args.limit,
+        batch_size_attribute='pageSize',
+        batch_size=args.limit,  # Use limit if any, else server default.
+        field='operations')

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

@@ -0,0 +1,48 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2018 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 genomics operations wait.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.api_lib.genomics import genomics_client
+from googlecloudsdk.api_lib.util import waiter
+from googlecloudsdk.calliope import base
+from googlecloudsdk.command_lib.genomics import flags
+
+
+class Wait(base.SilentCommand):
+  """Waits for an operation to complete.
+  """
+
+  @staticmethod
+  def Args(parser):
+    """Register flags for this command."""
+    flags.AddName(parser)
+
+  def Run(self, args):
+    """This is what gets called when the user runs this command.
+
+    Args:
+      args: an argparse namespace, All the arguments that were provided to this
+        command invocation.
+    """
+    client, resource = genomics_client.CreateFromName(args.name)
+    waiter.WaitFor(client.Poller(), resource,
+                   'Waiting for [{}]'.format(resource.RelativeName()),
+                   max_wait_ms=7 * 24 * 60 * 60 * 1000)
+    return None

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

@@ -0,0 +1,48 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2016 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.
+
+"""Genomics pipelines sub-group."""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+from googlecloudsdk.api_lib import genomics as lib
+from googlecloudsdk.api_lib.util import apis
+from googlecloudsdk.calliope import base
+
+
+class Pipelines(base.Group):
+  """Commands for Genomics pipelines.
+
+  Command to run a pipeline.
+  """
+
+  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/genomics/pipelines/run.py

@@ -0,0 +1,503 @@
+# -*- coding: utf-8 -*- #
+# Copyright 2016 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 genomics pipelines run.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+
+import base64
+from googlecloudsdk.api_lib import genomics as lib
+from googlecloudsdk.api_lib.genomics import exceptions
+from googlecloudsdk.api_lib.genomics import genomics_util
+from googlecloudsdk.calliope import arg_parsers
+from googlecloudsdk.calliope import base
+from googlecloudsdk.command_lib.util.args import labels_util
+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.GenomicsError(
+          '--{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):
+  """Defines and runs a pipeline.
+
+  A pipeline is a transformation of a set of inputs to a set of outputs.
+  Supports docker-based commands.
+  """
+
+  @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.
+    """
+    parser.add_argument(
+        '--pipeline-file',
+        help='''A YAML or JSON file containing a v2alpha1 Pipeline object. See
+[](https://cloud.google.com/genomics/reference/rest/v2alpha1/pipelines#Pipeline)
+''')
+
+    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(
+        '--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(
+        '--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(
+        '--memory',
+        category=base.COMMONLY_USED_FLAGS,
+        type=float,
+        help='''The number of GB of RAM needed to run the pipeline. Overrides
+             any value specified in the pipeline-file.''')
+
+    parser.add_argument(
+        '--cpus',
+        category=base.COMMONLY_USED_FLAGS,
+        type=int,
+        help='''The minimum number of CPUs to run the pipeline. Overrides
+             any value specified in the pipeline-file.''')
+
+    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 to 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/devstorage.read_write
+             https://www.googleapis.com/auth/genomics''')
+
+    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.
+
+If you have no default zone then at least one zone or region 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 accomondate 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.
+      GenomicsError: 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 = genomics_util.GetGenomicsClient('v2alpha1')
+    genomics_messages = genomics_util.GetGenomicsMessages('v2alpha1')
+    if args.pipeline_file:
+      if args.command_line:
+        # TODO(b/79982664): Use a mutex argument group instead.
+        raise exceptions.GenomicsError(
+            '--command-line cannot be used with --pipeline-file.')
+
+      pipeline = genomics_util.GetFileAsMessage(
+          args.pipeline_file,
+          genomics_messages.Pipeline,
+          self.context[lib.STORAGE_V1_CLIENT_KEY])
+    elif args.command_line:
+      pipeline = genomics_messages.Pipeline(
+          actions=[genomics_messages.Action(
+              imageUri=args.docker_image,
+              commands=['-c', args.command_line],
+              entrypoint='bash')])
+    else:
+      raise exceptions.GenomicsError(
+          'Either --pipeline-file or --command-line is required.')
+
+    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 = genomics_messages.Resources()
+    resources = pipeline.resources
+
+    if not resources.virtualMachine:
+      resources.virtualMachine = genomics_messages.VirtualMachine(
+          machineType='n1-standard-1')
+    virtual_machine = resources.virtualMachine
+
+    if not virtual_machine.serviceAccount:
+      virtual_machine.serviceAccount = genomics_messages.ServiceAccount()
+
+    # Always set the project id.
+    resources.projectId = genomics_util.GetProjectId()
+
+    # Update the pipeline based on arguments.
+    if args.memory or args.cpus:
+      # Default to n1-standard1 sizes.
+      virtual_machine.machineType = 'custom-%d-%d' % (args.cpus or 1,
+                                                      (args.memory or 3.75) *
+                                                      1024)
+
+    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 a scope for GCS in case any arguments need it.
+    virtual_machine.serviceAccount.scopes.append(
+        'https://www.googleapis.com/auth/devstorage.read_write')
+
+    # Attach custom network/subnetwork (if set).
+    if args.network or args.subnetwork:
+      if not virtual_machine.network:
+        virtual_machine.network = genomics_messages.Network()
+      if args.network:
+        virtual_machine.network.name = 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.GenomicsError(
+            '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 genomics_util.IsGcsPath(value):
+          env[name] = input_generator.Generate()
+          pipeline.actions.insert(
+              0,
+              genomics_messages.Action(
+                  imageUri=CLOUD_SDK_IMAGE,
+                  commands=[
+                      '/bin/sh', '-c',
+                      'gsutil -m -q cp %s ${%s}' % (value, name)
+                  ]))
+        elif name in is_local_file:
+          # TODO(b/183206325): Get test coverage to 100%.
+          env[name] = input_generator.Generate()
+          pipeline.actions.insert(
+              0,
+              genomics_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(
+            genomics_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 = genomics_messages.Pipeline.EnvironmentValue(
+        additionalProperties=genomics_util.ArgDictToAdditionalPropertiesList(
+            env,
+            genomics_messages.Pipeline.EnvironmentValue.AdditionalProperty))
+
+    if arg_inputs or args.outputs:
+      virtual_machine.disks.append(genomics_messages.Disk(name=SHARED_DISK))
+
+      for action in pipeline.actions:
+        action.mounts.append(
+            genomics_messages.Mount(disk=SHARED_DISK, path='/' + SHARED_DISK))
+
+    if args.logging:
+      pipeline.actions.append(
+          genomics_messages.Action(
+              imageUri=CLOUD_SDK_IMAGE,
+              commands=[
+                  '/bin/sh', '-c',
+                  'gsutil -m -q cp /google/logs/output ' + args.logging
+              ],
+              flags=[(genomics_messages.Action.FlagsValueListEntryValuesEnum
+                      .ALWAYS_RUN)]))
+
+    # 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.GenomicsError('Invalid --disk-size.')
+
+      for disk in virtual_machine.disks:
+        if disk.name in disk_sizes:
+          disk.sizeGb = disk_sizes[disk.name]
+
+    request = genomics_messages.RunPipelineRequest(
+        pipeline=pipeline,
+        labels=labels_util.ParseCreateArgs(
+            args, genomics_messages.RunPipelineRequest.LabelsValue))
+
+    result = apitools_client.pipelines.Run(request)
+    log.status.Print('Running [{0}].'.format(result.name))
+    return result