genomics

package
v0.0.0-...-2824937 Latest Latest
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 Go to latest Published: Nov 2, 2020 License: MIT, Apache-2.0 Imports: 11 Imported by: 0

Documentation

Overview

Package genomics is a generated protocol buffer package.

It is generated from these files: 

google/genomics/v1alpha2/pipelines.proto

It has these top-level messages: 

ComputeEngine
RuntimeMetadata
Pipeline
CreatePipelineRequest
RunPipelineArgs
RunPipelineRequest
GetPipelineRequest
ListPipelinesRequest
ListPipelinesResponse
DeletePipelineRequest
GetControllerConfigRequest
ControllerConfig
TimestampEvent
SetOperationStatusRequest
ServiceAccount
LoggingOptions
PipelineResources
PipelineParameter
DockerExecutor

Index

Constants

This section is empty.

Variables

View Source 
var PipelineResources_Disk_Type_name = map[int32]string{
	0: "TYPE_UNSPECIFIED",
	1: "PERSISTENT_HDD",
	2: "PERSISTENT_SSD",
	3: "LOCAL_SSD",
}
View Source 
var PipelineResources_Disk_Type_value = map[string]int32{
	"TYPE_UNSPECIFIED": 0,
	"PERSISTENT_HDD":   1,
	"PERSISTENT_SSD":   2,
	"LOCAL_SSD":        3,
}

Functions

func RegisterPipelinesV1Alpha2Server 

func RegisterPipelinesV1Alpha2Server(s *grpc.Server, srv PipelinesV1Alpha2Server)

Types

type ComputeEngine 

type ComputeEngine struct {
	// The instance on which the operation is running.
	InstanceName string `protobuf:"bytes,1,opt,name=instance_name,json=instanceName" json:"instance_name,omitempty"`
	// The availability zone in which the instance resides.
	Zone string `protobuf:"bytes,2,opt,name=zone" json:"zone,omitempty"`
	// The machine type of the instance.
	MachineType string `protobuf:"bytes,3,opt,name=machine_type,json=machineType" json:"machine_type,omitempty"`
	// The names of the disks that were created for this pipeline.
	DiskNames []string `protobuf:"bytes,4,rep,name=disk_names,json=diskNames" json:"disk_names,omitempty"`
}

Describes a Compute Engine resource that is being managed by a running [pipeline][google.genomics.v1alpha2.Pipeline].

func (*ComputeEngine) Descriptor 

func (*ComputeEngine) Descriptor() ([]byte, []int)

func (*ComputeEngine) GetDiskNames 

func (m *ComputeEngine) GetDiskNames() []string

func (*ComputeEngine) GetInstanceName 

func (m *ComputeEngine) GetInstanceName() string

func (*ComputeEngine) GetMachineType 

func (m *ComputeEngine) GetMachineType() string

func (*ComputeEngine) GetZone 

func (m *ComputeEngine) GetZone() string

func (*ComputeEngine) ProtoMessage 

func (*ComputeEngine) ProtoMessage()

func (*ComputeEngine) Reset 

func (m *ComputeEngine) Reset()

func (*ComputeEngine) String 

func (m *ComputeEngine) String() string

type ControllerConfig 

type ControllerConfig struct {
	Image       string                                      `protobuf:"bytes,1,opt,name=image" json:"image,omitempty"`
	Cmd         string                                      `protobuf:"bytes,2,opt,name=cmd" json:"cmd,omitempty"`
	GcsLogPath  string                                      `protobuf:"bytes,3,opt,name=gcs_log_path,json=gcsLogPath" json:"gcs_log_path,omitempty"`
	MachineType string                                      `protobuf:"bytes,4,opt,name=machine_type,json=machineType" json:"machine_type,omitempty"`
	Vars        map[string]string                           `` /* 128-byte string literal not displayed */
	Disks       map[string]string                           `` /* 130-byte string literal not displayed */
	GcsSources  map[string]*ControllerConfig_RepeatedString `` /* 158-byte string literal not displayed */
	GcsSinks    map[string]*ControllerConfig_RepeatedString `` /* 152-byte string literal not displayed */
}

Stores the information that the controller will fetch from the server in order to run. Should only be used by VMs created by the Pipelines Service and not by end users.

func (*ControllerConfig) Descriptor 

func (*ControllerConfig) Descriptor() ([]byte, []int)

func (*ControllerConfig) GetCmd 

func (m *ControllerConfig) GetCmd() string

func (*ControllerConfig) GetDisks 

func (m *ControllerConfig) GetDisks() map[string]string

func (*ControllerConfig) GetGcsLogPath 

func (m *ControllerConfig) GetGcsLogPath() string

func (*ControllerConfig) GetGcsSinks 

func (m *ControllerConfig) GetGcsSinks() map[string]*ControllerConfig_RepeatedString

func (*ControllerConfig) GetGcsSources 

func (m *ControllerConfig) GetGcsSources() map[string]*ControllerConfig_RepeatedString

func (*ControllerConfig) GetImage 

func (m *ControllerConfig) GetImage() string

func (*ControllerConfig) GetMachineType 

func (m *ControllerConfig) GetMachineType() string

func (*ControllerConfig) GetVars 

func (m *ControllerConfig) GetVars() map[string]string

func (*ControllerConfig) ProtoMessage 

func (*ControllerConfig) ProtoMessage()

func (*ControllerConfig) Reset 

func (m *ControllerConfig) Reset()

func (*ControllerConfig) String 

func (m *ControllerConfig) String() string

type ControllerConfig_RepeatedString 

type ControllerConfig_RepeatedString struct {
	Values []string `protobuf:"bytes,1,rep,name=values" json:"values,omitempty"`
}

func (*ControllerConfig_RepeatedString) Descriptor 

func (*ControllerConfig_RepeatedString) Descriptor() ([]byte, []int)

func (*ControllerConfig_RepeatedString) GetValues 

func (m *ControllerConfig_RepeatedString) GetValues() []string

func (*ControllerConfig_RepeatedString) ProtoMessage 

func (*ControllerConfig_RepeatedString) ProtoMessage()

func (*ControllerConfig_RepeatedString) Reset 

func (m *ControllerConfig_RepeatedString) Reset()

func (*ControllerConfig_RepeatedString) String 

func (m *ControllerConfig_RepeatedString) String() string

type CreatePipelineRequest 

type CreatePipelineRequest struct {
	// The pipeline to create. Should not have `pipelineId` populated.
	Pipeline *Pipeline `protobuf:"bytes,1,opt,name=pipeline" json:"pipeline,omitempty"`
}

The request to create a pipeline. The pipeline field here should not have `pipelineId` populated, as that will be populated by the server.

func (*CreatePipelineRequest) Descriptor 

func (*CreatePipelineRequest) Descriptor() ([]byte, []int)

func (*CreatePipelineRequest) GetPipeline 

func (m *CreatePipelineRequest) GetPipeline() *Pipeline

func (*CreatePipelineRequest) ProtoMessage 

func (*CreatePipelineRequest) ProtoMessage()

func (*CreatePipelineRequest) Reset 

func (m *CreatePipelineRequest) Reset()

func (*CreatePipelineRequest) String 

func (m *CreatePipelineRequest) String() string

type DeletePipelineRequest 

type DeletePipelineRequest struct {
	// Caller must have WRITE access to the project in which this pipeline
	// is defined.
	PipelineId string `protobuf:"bytes,1,opt,name=pipeline_id,json=pipelineId" json:"pipeline_id,omitempty"`
}

The request to delete a saved pipeline by ID.

func (*DeletePipelineRequest) Descriptor 

func (*DeletePipelineRequest) Descriptor() ([]byte, []int)

func (*DeletePipelineRequest) GetPipelineId 

func (m *DeletePipelineRequest) GetPipelineId() string

func (*DeletePipelineRequest) ProtoMessage 

func (*DeletePipelineRequest) ProtoMessage()

func (*DeletePipelineRequest) Reset 

func (m *DeletePipelineRequest) Reset()

func (*DeletePipelineRequest) String 

func (m *DeletePipelineRequest) String() string

type DockerExecutor 

type DockerExecutor struct {
	// Required. Image name from either Docker Hub or Google Container Registry.
	// Users that run pipelines must have READ access to the image.
	ImageName string `protobuf:"bytes,1,opt,name=image_name,json=imageName" json:"image_name,omitempty"`
	// Required. The command or newline delimited script to run. The command
	// string will be executed within a bash shell.
	//
	// If the command exits with a non-zero exit code, output parameter
	// de-localization will be skipped and the pipeline operation's
	// [`error`][google.longrunning.Operation.error] field will be populated.
	//
	// Maximum command string length is 16384.
	Cmd string `protobuf:"bytes,2,opt,name=cmd" json:"cmd,omitempty"`
}

The Docker execuctor specification.

func (*DockerExecutor) Descriptor 

func (*DockerExecutor) Descriptor() ([]byte, []int)

func (*DockerExecutor) GetCmd 

func (m *DockerExecutor) GetCmd() string

func (*DockerExecutor) GetImageName 

func (m *DockerExecutor) GetImageName() string

func (*DockerExecutor) ProtoMessage 

func (*DockerExecutor) ProtoMessage()

func (*DockerExecutor) Reset 

func (m *DockerExecutor) Reset()

func (*DockerExecutor) String 

func (m *DockerExecutor) String() string

type GetControllerConfigRequest 

type GetControllerConfigRequest struct {
	// The operation to retrieve controller configuration for.
	OperationId     string `protobuf:"bytes,1,opt,name=operation_id,json=operationId" json:"operation_id,omitempty"`
	ValidationToken uint64 `protobuf:"varint,2,opt,name=validation_token,json=validationToken" json:"validation_token,omitempty"`
}

Request to get controller configuation. Should only be used by VMs created by the Pipelines Service and not by end users.

func (*GetControllerConfigRequest) Descriptor 

func (*GetControllerConfigRequest) Descriptor() ([]byte, []int)

func (*GetControllerConfigRequest) GetOperationId 

func (m *GetControllerConfigRequest) GetOperationId() string

func (*GetControllerConfigRequest) GetValidationToken 

func (m *GetControllerConfigRequest) GetValidationToken() uint64

func (*GetControllerConfigRequest) ProtoMessage 

func (*GetControllerConfigRequest) ProtoMessage()

func (*GetControllerConfigRequest) Reset 

func (m *GetControllerConfigRequest) Reset()

func (*GetControllerConfigRequest) String 

func (m *GetControllerConfigRequest) String() string

type GetPipelineRequest 

type GetPipelineRequest struct {
	// Caller must have READ access to the project in which this pipeline
	// is defined.
	PipelineId string `protobuf:"bytes,1,opt,name=pipeline_id,json=pipelineId" json:"pipeline_id,omitempty"`
}

A request to get a saved pipeline by id.

func (*GetPipelineRequest) Descriptor 

func (*GetPipelineRequest) Descriptor() ([]byte, []int)

func (*GetPipelineRequest) GetPipelineId 

func (m *GetPipelineRequest) GetPipelineId() string

func (*GetPipelineRequest) ProtoMessage 

func (*GetPipelineRequest) ProtoMessage()

func (*GetPipelineRequest) Reset 

func (m *GetPipelineRequest) Reset()

func (*GetPipelineRequest) String 

func (m *GetPipelineRequest) String() string

type ListPipelinesRequest 

type ListPipelinesRequest struct {
	// Required. The name of the project to search for pipelines. Caller
	// must have READ access to this project.
	ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId" json:"project_id,omitempty"`
	// Pipelines with names that match this prefix should be
	// returned.  If unspecified, all pipelines in the project, up to
	// `pageSize`, will be returned.
	NamePrefix string `protobuf:"bytes,2,opt,name=name_prefix,json=namePrefix" json:"name_prefix,omitempty"`
	// Number of pipelines to return at once. Defaults to 256, and max
	// is 2048.
	PageSize int32 `protobuf:"varint,3,opt,name=page_size,json=pageSize" json:"page_size,omitempty"`
	// Token to use to indicate where to start getting results.
	// If unspecified, returns the first page of results.
	PageToken string `protobuf:"bytes,4,opt,name=page_token,json=pageToken" json:"page_token,omitempty"`
}

A request to list pipelines in a given project. Pipelines can be filtered by name using `namePrefix`: all pipelines with names that begin with `namePrefix` will be returned. Uses standard pagination: `pageSize` indicates how many pipelines to return, and `pageToken` comes from a previous ListPipelinesResponse to indicate offset.

func (*ListPipelinesRequest) Descriptor 

func (*ListPipelinesRequest) Descriptor() ([]byte, []int)

func (*ListPipelinesRequest) GetNamePrefix 

func (m *ListPipelinesRequest) GetNamePrefix() string

func (*ListPipelinesRequest) GetPageSize 

func (m *ListPipelinesRequest) GetPageSize() int32

func (*ListPipelinesRequest) GetPageToken 

func (m *ListPipelinesRequest) GetPageToken() string

func (*ListPipelinesRequest) GetProjectId 

func (m *ListPipelinesRequest) GetProjectId() string

func (*ListPipelinesRequest) ProtoMessage 

func (*ListPipelinesRequest) ProtoMessage()

func (*ListPipelinesRequest) Reset 

func (m *ListPipelinesRequest) Reset()

func (*ListPipelinesRequest) String 

func (m *ListPipelinesRequest) String() string

type ListPipelinesResponse 

type ListPipelinesResponse struct {
	// The matched pipelines.
	Pipelines []*Pipeline `protobuf:"bytes,1,rep,name=pipelines" json:"pipelines,omitempty"`
	// The token to use to get the next page of results.
	NextPageToken string `protobuf:"bytes,2,opt,name=next_page_token,json=nextPageToken" json:"next_page_token,omitempty"`
}

The response of ListPipelines. Contains at most `pageSize` pipelines. If it contains `pageSize` pipelines, and more pipelines exist, then `nextPageToken` will be populated and should be used as the `pageToken` argument to a subsequent ListPipelines request.

func (*ListPipelinesResponse) Descriptor 

func (*ListPipelinesResponse) Descriptor() ([]byte, []int)

func (*ListPipelinesResponse) GetNextPageToken 

func (m *ListPipelinesResponse) GetNextPageToken() string

func (*ListPipelinesResponse) GetPipelines 

func (m *ListPipelinesResponse) GetPipelines() []*Pipeline

func (*ListPipelinesResponse) ProtoMessage 

func (*ListPipelinesResponse) ProtoMessage()

func (*ListPipelinesResponse) Reset 

func (m *ListPipelinesResponse) Reset()

func (*ListPipelinesResponse) String 

func (m *ListPipelinesResponse) String() string

type LoggingOptions 

type LoggingOptions struct {
	// 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, and the user must ensure that logs are not
	// overwritten. Stdout and stderr logs from the run are also
	// generated and output as `-stdout.log` and `-stderr.log`.
	GcsPath string `protobuf:"bytes,1,opt,name=gcs_path,json=gcsPath" json:"gcs_path,omitempty"`
}

The logging options for the pipeline run.

func (*LoggingOptions) Descriptor 

func (*LoggingOptions) Descriptor() ([]byte, []int)

func (*LoggingOptions) GetGcsPath 

func (m *LoggingOptions) GetGcsPath() string

func (*LoggingOptions) ProtoMessage 

func (*LoggingOptions) ProtoMessage()

func (*LoggingOptions) Reset 

func (m *LoggingOptions) Reset()

func (*LoggingOptions) String 

func (m *LoggingOptions) String() string

type Pipeline 

type Pipeline struct {
	// Required. The project in which to create the pipeline. The caller must have
	// WRITE access.
	ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId" json:"project_id,omitempty"`
	// Required. A user specified pipeline name that does not have to be unique.
	// This name can be used for filtering Pipelines in ListPipelines.
	Name string `protobuf:"bytes,2,opt,name=name" json:"name,omitempty"`
	// User-specified description.
	Description string `protobuf:"bytes,3,opt,name=description" json:"description,omitempty"`
	// Input parameters of the pipeline.
	InputParameters []*PipelineParameter `protobuf:"bytes,8,rep,name=input_parameters,json=inputParameters" json:"input_parameters,omitempty"`
	// Output parameters of the pipeline.
	OutputParameters []*PipelineParameter `protobuf:"bytes,9,rep,name=output_parameters,json=outputParameters" json:"output_parameters,omitempty"`
	// Required. The executor indicates in which environment the pipeline runs.
	//
	// Types that are valid to be assigned to Executor:
	//	*Pipeline_Docker
	Executor isPipeline_Executor `protobuf_oneof:"executor"`
	// Required. Specifies resource requirements for the pipeline run.
	// Required fields:
	//
	// *
	// [minimumCpuCores][google.genomics.v1alpha2.PipelineResources.minimum_cpu_cores]
	//
	// *
	// [minimumRamGb][google.genomics.v1alpha2.PipelineResources.minimum_ram_gb]
	Resources *PipelineResources `protobuf:"bytes,6,opt,name=resources" json:"resources,omitempty"`
	// Unique pipeline id that is generated by the service when CreatePipeline
	// is called. Cannot be specified in the Pipeline used in the
	// CreatePipelineRequest, and will be populated in the response to
	// CreatePipeline and all subsequent Get and List calls. Indicates that the
	// service has registered this pipeline.
	PipelineId string `protobuf:"bytes,7,opt,name=pipeline_id,json=pipelineId" json:"pipeline_id,omitempty"`
}

The pipeline object. Represents a transformation from a set of input parameters to a set of output parameters. The transformation is defined as a docker image and command to run within that image. Each pipeline is run on a Google Compute Engine VM. A pipeline can be created with the `create` method and then later run with the `run` method, or a pipeline can be defined and run all at once with the `run` method.

func (*Pipeline) Descriptor 

func (*Pipeline) Descriptor() ([]byte, []int)

func (*Pipeline) GetDescription 

func (m *Pipeline) GetDescription() string

func (*Pipeline) GetDocker 

func (m *Pipeline) GetDocker() *DockerExecutor

func (*Pipeline) GetExecutor 

func (m *Pipeline) GetExecutor() isPipeline_Executor

func (*Pipeline) GetInputParameters 

func (m *Pipeline) GetInputParameters() []*PipelineParameter

func (*Pipeline) GetName 

func (m *Pipeline) GetName() string

func (*Pipeline) GetOutputParameters 

func (m *Pipeline) GetOutputParameters() []*PipelineParameter

func (*Pipeline) GetPipelineId 

func (m *Pipeline) GetPipelineId() string

func (*Pipeline) GetProjectId 

func (m *Pipeline) GetProjectId() string

func (*Pipeline) GetResources 

func (m *Pipeline) GetResources() *PipelineResources

func (*Pipeline) ProtoMessage 

func (*Pipeline) ProtoMessage()

func (*Pipeline) Reset 

func (m *Pipeline) Reset()

func (*Pipeline) String 

func (m *Pipeline) String() string

func (*Pipeline) XXX_OneofFuncs 

func (*Pipeline) XXX_OneofFuncs() (func(msg proto.Message, b *proto.Buffer) error, func(msg proto.Message, tag, wire int, b *proto.Buffer) (bool, error), func(msg proto.Message) (n int), []interface{})

XXX_OneofFuncs is for the internal use of the proto package.

type PipelineParameter 

type PipelineParameter struct {
	// Required. Name of the parameter - the pipeline runner uses this string
	// as the key to the input and output maps in RunPipeline.
	Name string `protobuf:"bytes,1,opt,name=name" json:"name,omitempty"`
	// Human-readable description.
	Description string `protobuf:"bytes,2,opt,name=description" json:"description,omitempty"`
	// The default value for this parameter. Can be overridden at runtime.
	// If `localCopy` is present, then this must be a Google Cloud Storage path
	// beginning with `gs://`.
	DefaultValue string `protobuf:"bytes,5,opt,name=default_value,json=defaultValue" json:"default_value,omitempty"`
	// If present, this parameter is marked for copying to and from the VM.
	// `LocalCopy` indicates where on the VM the file should be. The value
	// given to this parameter (either at runtime or using `defaultValue`)
	// must be the remote path where the file should be.
	LocalCopy *PipelineParameter_LocalCopy `protobuf:"bytes,6,opt,name=local_copy,json=localCopy" json:"local_copy,omitempty"`
}

Parameters facilitate setting and delivering data into the pipeline's execution environment. They are defined at create time, with optional defaults, and can be overridden at run time.

If `localCopy` is unset, then the parameter specifies a string that is passed as-is into the pipeline, as the value of the environment variable with the given name. A default value can be optionally specified at create time. The default can be overridden at run time using the inputs map. If no default is given, a value must be supplied at runtime.

If `localCopy` is defined, then the parameter specifies a data source or sink, both in Google Cloud Storage and on the Docker container where the pipeline computation is run. The [service account associated with the Pipeline][google.genomics.v1alpha2.RunPipelineArgs.service_account] (by default the project's Compute Engine service account) must have access to the Google Cloud Storage paths.

At run time, the Google Cloud Storage paths can be overridden if a default was provided at create time, or must be set otherwise. The pipeline runner should add a key/value pair to either the inputs or outputs map. The indicated data copies will be carried out before/after pipeline execution, just as if the corresponding arguments were provided to `gsutil cp`.

For example: Given the following `PipelineParameter`, specified in the `inputParameters` list:

``` {name: "input_file", localCopy: {path: "file.txt", disk: "pd1"}} ```

where `disk` is defined in the `PipelineResources` object as:

``` {name: "pd1", mountPoint: "/mnt/disk/"} ```

We create a disk named `pd1`, mount it on the host VM, and map `/mnt/pd1` to `/mnt/disk` in the docker container. At runtime, an entry for `input_file` would be required in the inputs map, such as:

``` 

inputs["input_file"] = "gs://my-bucket/bar.txt"

```

This would generate the following gsutil call:

``` 

gsutil cp gs://my-bucket/bar.txt /mnt/pd1/file.txt

```

The file `/mnt/pd1/file.txt` maps to `/mnt/disk/file.txt` in the Docker container. Acceptable paths are:

<table> 

<thead>
  <tr><th>Google Cloud storage path</th><th>Local path</th></tr>
</thead>
<tbody>
  <tr><td>file</td><td>file</td></tr>
  <tr><td>glob</td><td>directory</td></tr>
</tbody>

</table>

For outputs, the direction of the copy is reversed:

``` 

gsutil cp /mnt/disk/file.txt gs://my-bucket/bar.txt

```

Acceptable paths are:

<table> 

<thead>
  <tr><th>Local path</th><th>Google Cloud Storage path</th></tr>
</thead>
<tbody>
  <tr><td>file</td><td>file</td></tr>
  <tr>
    <td>file</td>
    <td>directory - directory must already exist</td>
  </tr>
  <tr>
    <td>glob</td>
    <td>directory - directory will be created if it doesn't exist</td></tr>
</tbody>

</table>

One restriction due to docker limitations, is that for outputs that are found on the boot disk, the local path cannot be a glob and must be a file.

func (*PipelineParameter) Descriptor 

func (*PipelineParameter) Descriptor() ([]byte, []int)

func (*PipelineParameter) GetDefaultValue 

func (m *PipelineParameter) GetDefaultValue() string

func (*PipelineParameter) GetDescription 

func (m *PipelineParameter) GetDescription() string

func (*PipelineParameter) GetLocalCopy 

func (m *PipelineParameter) GetLocalCopy() *PipelineParameter_LocalCopy

func (*PipelineParameter) GetName 

func (m *PipelineParameter) GetName() string

func (*PipelineParameter) ProtoMessage 

func (*PipelineParameter) ProtoMessage()

func (*PipelineParameter) Reset 

func (m *PipelineParameter) Reset()

func (*PipelineParameter) String 

func (m *PipelineParameter) String() string

type PipelineParameter_LocalCopy 

type PipelineParameter_LocalCopy struct {
	// Required. The path within the user's docker container where
	// this input should be localized to and from, relative to the specified
	// disk's mount point. For example: file.txt,
	Path string `protobuf:"bytes,1,opt,name=path" json:"path,omitempty"`
	// Required. The name of the disk where this parameter is
	// located. Can be the name of one of the disks specified in the
	// Resources field, or "boot", which represents the Docker
	// instance's boot disk and has a mount point of `/`.
	Disk string `protobuf:"bytes,2,opt,name=disk" json:"disk,omitempty"`
}

LocalCopy defines how a remote file should be copied to and from the VM.

func (*PipelineParameter_LocalCopy) Descriptor 

func (*PipelineParameter_LocalCopy) Descriptor() ([]byte, []int)

func (*PipelineParameter_LocalCopy) GetDisk 

func (m *PipelineParameter_LocalCopy) GetDisk() string

func (*PipelineParameter_LocalCopy) GetPath 

func (m *PipelineParameter_LocalCopy) GetPath() string

func (*PipelineParameter_LocalCopy) ProtoMessage 

func (*PipelineParameter_LocalCopy) ProtoMessage()

func (*PipelineParameter_LocalCopy) Reset 

func (m *PipelineParameter_LocalCopy) Reset()

func (*PipelineParameter_LocalCopy) String 

func (m *PipelineParameter_LocalCopy) String() string

type PipelineResources 

type PipelineResources struct {
	// The minimum number of cores to use. Defaults to 1.
	MinimumCpuCores int32 `protobuf:"varint,1,opt,name=minimum_cpu_cores,json=minimumCpuCores" json:"minimum_cpu_cores,omitempty"`
	// Whether to use preemptible VMs. Defaults to `false`. In order to use this,
	// must be true for both create time and run time. Cannot be true at run time
	// if false at create time.
	Preemptible bool `protobuf:"varint,2,opt,name=preemptible" json:"preemptible,omitempty"`
	// The minimum amount of RAM to use. Defaults to 3.75 (GB)
	MinimumRamGb float64 `protobuf:"fixed64,3,opt,name=minimum_ram_gb,json=minimumRamGb" json:"minimum_ram_gb,omitempty"`
	// Disks to attach.
	Disks []*PipelineResources_Disk `protobuf:"bytes,4,rep,name=disks" json:"disks,omitempty"`
	// List of Google Compute Engine availability zones to which resource
	// creation will restricted. If empty, any zone may be chosen.
	Zones []string `protobuf:"bytes,5,rep,name=zones" json:"zones,omitempty"`
	// The size of the boot disk. Defaults to 10 (GB).
	BootDiskSizeGb int32 `protobuf:"varint,6,opt,name=boot_disk_size_gb,json=bootDiskSizeGb" json:"boot_disk_size_gb,omitempty"`
	// Whether to assign an external IP to the instance. This is an experimental
	// feature that may go away. Defaults to false.
	// Corresponds to `--no_address` flag for [gcloud compute instances create]
	// (https://cloud.google.com/sdk/gcloud/reference/compute/instances/create).
	// In order to use this, must be true for both create time and run time.
	// Cannot be true at run time if false at create time. If you need to ssh into
	// a private IP VM for debugging, you can ssh to a public VM and then ssh into
	// the private VM's Internal IP.  If noAddress is set, this pipeline run may
	// only load docker images from Google Container Registry and not Docker Hub.
	// ** Note: To use this option, your project must be in Google Access for
	// Private IPs Early Access Program.**
	NoAddress bool `protobuf:"varint,7,opt,name=no_address,json=noAddress" json:"no_address,omitempty"`
}

The system resources for the pipeline run.

func (*PipelineResources) Descriptor 

func (*PipelineResources) Descriptor() ([]byte, []int)

func (*PipelineResources) GetBootDiskSizeGb 

func (m *PipelineResources) GetBootDiskSizeGb() int32

func (*PipelineResources) GetDisks 

func (m *PipelineResources) GetDisks() []*PipelineResources_Disk

func (*PipelineResources) GetMinimumCpuCores 

func (m *PipelineResources) GetMinimumCpuCores() int32

func (*PipelineResources) GetMinimumRamGb 

func (m *PipelineResources) GetMinimumRamGb() float64

func (*PipelineResources) GetNoAddress 

func (m *PipelineResources) GetNoAddress() bool

func (*PipelineResources) GetPreemptible 

func (m *PipelineResources) GetPreemptible() bool

func (*PipelineResources) GetZones 

func (m *PipelineResources) GetZones() []string

func (*PipelineResources) ProtoMessage 

func (*PipelineResources) ProtoMessage()

func (*PipelineResources) Reset 

func (m *PipelineResources) Reset()

func (*PipelineResources) String 

func (m *PipelineResources) String() string

type PipelineResources_Disk 

type PipelineResources_Disk struct {
	// Required. The name of the disk that can be used in the pipeline
	// parameters. Must be 1 - 63 characters.
	// The name "boot" is reserved for system use.
	Name string `protobuf:"bytes,1,opt,name=name" json:"name,omitempty"`
	// Required. The type of the disk to create.
	Type PipelineResources_Disk_Type `protobuf:"varint,2,opt,name=type,enum=google.genomics.v1alpha2.PipelineResources_Disk_Type" json:"type,omitempty"`
	// The size of the disk. Defaults to 500 (GB).
	// This field is not applicable for local SSD.
	SizeGb int32 `protobuf:"varint,3,opt,name=size_gb,json=sizeGb" json:"size_gb,omitempty"`
	// The full or partial URL of the persistent disk to attach. See
	// https://cloud.google.com/compute/docs/reference/latest/instances#resource
	// and
	// https://cloud.google.com/compute/docs/disks/persistent-disks#snapshots
	// for more details.
	Source string `protobuf:"bytes,4,opt,name=source" json:"source,omitempty"`
	// Deprecated. Disks created by the Pipelines API will be deleted at the end
	// of the pipeline run, regardless of what this field is set to.
	AutoDelete bool `protobuf:"varint,6,opt,name=auto_delete,json=autoDelete" json:"auto_delete,omitempty"`
	// Required at create time and cannot be overridden at run time.
	// Specifies the path in the docker container where files on
	// this disk should be located. For example, if `mountPoint`
	// is `/mnt/disk`, and the parameter has `localPath`
	// `inputs/file.txt`, the docker container can access the data at
	// `/mnt/disk/inputs/file.txt`.
	MountPoint string `protobuf:"bytes,8,opt,name=mount_point,json=mountPoint" json:"mount_point,omitempty"`
}

A Google Compute Engine disk resource specification.

func (*PipelineResources_Disk) Descriptor 

func (*PipelineResources_Disk) Descriptor() ([]byte, []int)

func (*PipelineResources_Disk) GetAutoDelete 

func (m *PipelineResources_Disk) GetAutoDelete() bool

func (*PipelineResources_Disk) GetMountPoint 

func (m *PipelineResources_Disk) GetMountPoint() string

func (*PipelineResources_Disk) GetName 

func (m *PipelineResources_Disk) GetName() string

func (*PipelineResources_Disk) GetSizeGb 

func (m *PipelineResources_Disk) GetSizeGb() int32

func (*PipelineResources_Disk) GetSource 

func (m *PipelineResources_Disk) GetSource() string

func (*PipelineResources_Disk) GetType 

func (m *PipelineResources_Disk) GetType() PipelineResources_Disk_Type

func (*PipelineResources_Disk) ProtoMessage 

func (*PipelineResources_Disk) ProtoMessage()

func (*PipelineResources_Disk) Reset 

func (m *PipelineResources_Disk) Reset()

func (*PipelineResources_Disk) String 

func (m *PipelineResources_Disk) String() string

type PipelineResources_Disk_Type 

type PipelineResources_Disk_Type int32

The types of disks that may be attached to VMs. 

const (
	// Default disk type. Use one of the other options below.
	PipelineResources_Disk_TYPE_UNSPECIFIED PipelineResources_Disk_Type = 0
	// Specifies a Google Compute Engine persistent hard disk. See
	// https://cloud.google.com/compute/docs/disks/#pdspecs for details.
	PipelineResources_Disk_PERSISTENT_HDD PipelineResources_Disk_Type = 1
	// Specifies a Google Compute Engine persistent solid-state disk. See
	// https://cloud.google.com/compute/docs/disks/#pdspecs for details.
	PipelineResources_Disk_PERSISTENT_SSD PipelineResources_Disk_Type = 2
	// Specifies a Google Compute Engine local SSD.
	// See https://cloud.google.com/compute/docs/disks/local-ssd for details.
	PipelineResources_Disk_LOCAL_SSD PipelineResources_Disk_Type = 3
)

func (PipelineResources_Disk_Type) EnumDescriptor 

func (PipelineResources_Disk_Type) EnumDescriptor() ([]byte, []int)

func (PipelineResources_Disk_Type) String 

func (x PipelineResources_Disk_Type) String() string

type Pipeline_Docker 

type Pipeline_Docker struct {
	Docker *DockerExecutor `protobuf:"bytes,5,opt,name=docker,oneof"`
}

type PipelinesV1Alpha2Client 

type PipelinesV1Alpha2Client interface {
	// Creates a pipeline that can be run later. Create takes a Pipeline that
	// has all fields other than `pipelineId` populated, and then returns
	// the same pipeline with `pipelineId` populated. This id can be used
	// to run the pipeline.
	//
	// Caller must have WRITE permission to the project.
	CreatePipeline(ctx context.Context, in *CreatePipelineRequest, opts ...grpc.CallOption) (*Pipeline, error)
	// Runs a pipeline. If `pipelineId` is specified in the request, then
	// run a saved pipeline. If `ephemeralPipeline` is specified, then run
	// that pipeline once without saving a copy.
	//
	// The caller must have READ permission to the project where the pipeline
	// is stored and WRITE permission to the project where the pipeline will be
	// run, as VMs will be created and storage will be used.
	RunPipeline(ctx context.Context, in *RunPipelineRequest, opts ...grpc.CallOption) (*google_longrunning.Operation, error)
	// Retrieves a pipeline based on ID.
	//
	// Caller must have READ permission to the project.
	GetPipeline(ctx context.Context, in *GetPipelineRequest, opts ...grpc.CallOption) (*Pipeline, error)
	// Lists pipelines.
	//
	// Caller must have READ permission to the project.
	ListPipelines(ctx context.Context, in *ListPipelinesRequest, opts ...grpc.CallOption) (*ListPipelinesResponse, error)
	// Deletes a pipeline based on ID.
	//
	// Caller must have WRITE permission to the project.
	DeletePipeline(ctx context.Context, in *DeletePipelineRequest, opts ...grpc.CallOption) (*google_protobuf2.Empty, error)
	// Gets controller configuration information. Should only be called
	// by VMs created by the Pipelines Service and not by end users.
	GetControllerConfig(ctx context.Context, in *GetControllerConfigRequest, opts ...grpc.CallOption) (*ControllerConfig, error)
	// Sets status of a given operation. Any new timestamps (as determined by
	// description) are appended to TimestampEvents. Should only be called by VMs
	// created by the Pipelines Service and not by end users.
	SetOperationStatus(ctx context.Context, in *SetOperationStatusRequest, opts ...grpc.CallOption) (*google_protobuf2.Empty, error)
}

func NewPipelinesV1Alpha2Client 

func NewPipelinesV1Alpha2Client(cc *grpc.ClientConn) PipelinesV1Alpha2Client

type PipelinesV1Alpha2Server 

type PipelinesV1Alpha2Server interface {
	// Creates a pipeline that can be run later. Create takes a Pipeline that
	// has all fields other than `pipelineId` populated, and then returns
	// the same pipeline with `pipelineId` populated. This id can be used
	// to run the pipeline.
	//
	// Caller must have WRITE permission to the project.
	CreatePipeline(context.Context, *CreatePipelineRequest) (*Pipeline, error)
	// Runs a pipeline. If `pipelineId` is specified in the request, then
	// run a saved pipeline. If `ephemeralPipeline` is specified, then run
	// that pipeline once without saving a copy.
	//
	// The caller must have READ permission to the project where the pipeline
	// is stored and WRITE permission to the project where the pipeline will be
	// run, as VMs will be created and storage will be used.
	RunPipeline(context.Context, *RunPipelineRequest) (*google_longrunning.Operation, error)
	// Retrieves a pipeline based on ID.
	//
	// Caller must have READ permission to the project.
	GetPipeline(context.Context, *GetPipelineRequest) (*Pipeline, error)
	// Lists pipelines.
	//
	// Caller must have READ permission to the project.
	ListPipelines(context.Context, *ListPipelinesRequest) (*ListPipelinesResponse, error)
	// Deletes a pipeline based on ID.
	//
	// Caller must have WRITE permission to the project.
	DeletePipeline(context.Context, *DeletePipelineRequest) (*google_protobuf2.Empty, error)
	// Gets controller configuration information. Should only be called
	// by VMs created by the Pipelines Service and not by end users.
	GetControllerConfig(context.Context, *GetControllerConfigRequest) (*ControllerConfig, error)
	// Sets status of a given operation. Any new timestamps (as determined by
	// description) are appended to TimestampEvents. Should only be called by VMs
	// created by the Pipelines Service and not by end users.
	SetOperationStatus(context.Context, *SetOperationStatusRequest) (*google_protobuf2.Empty, error)
}

type RunPipelineArgs 

type RunPipelineArgs struct {
	// Required. The project in which to run the pipeline. The caller must have
	// WRITER access to all Google Cloud services and resources (e.g. Google
	// Compute Engine) will be used.
	ProjectId string `protobuf:"bytes,1,opt,name=project_id,json=projectId" json:"project_id,omitempty"`
	// Pipeline input arguments; keys are defined in the pipeline documentation.
	// All input parameters that do not have default values  must be specified.
	// If parameters with defaults are specified here, the defaults will be
	// overridden.
	Inputs map[string]string `` /* 132-byte string literal not displayed */
	// Pipeline output arguments; keys are defined in the pipeline
	// documentation.  All output parameters of without default values
	// must be specified.  If parameters with defaults are specified
	// here, the defaults will be overridden.
	Outputs map[string]string `` /* 134-byte string literal not displayed */
	// The Google Cloud Service Account that will be used to access data and
	// services. By default, the compute service account associated with
	// `projectId` is used.
	ServiceAccount *ServiceAccount `protobuf:"bytes,4,opt,name=service_account,json=serviceAccount" json:"service_account,omitempty"`
	// This field is deprecated. Use `labels` instead. Client-specified pipeline
	// operation identifier.
	ClientId string `protobuf:"bytes,5,opt,name=client_id,json=clientId" json:"client_id,omitempty"`
	// Specifies resource requirements/overrides for the pipeline run.
	Resources *PipelineResources `protobuf:"bytes,6,opt,name=resources" json:"resources,omitempty"`
	// Required. Logging options. Used by the service to communicate results
	// to the user.
	Logging *LoggingOptions `protobuf:"bytes,7,opt,name=logging" json:"logging,omitempty"`
	// How long to keep the VM up after a failure (for example docker command
	// failed, copying input or output files failed, etc). While the VM is up, one
	// can ssh into the VM to debug. Default is 0; maximum allowed value is 1 day.
	KeepVmAliveOnFailureDuration *google_protobuf3.Duration `` /* 146-byte string literal not displayed */
	// Labels to apply to this pipeline run. Labels will also be applied to
	// compute resources (VM, disks) created by this pipeline run. When listing
	// operations, operations can [filtered by labels]
	// [google.longrunning.ListOperationsRequest.filter].
	// Label keys may not be empty; label values may be empty. Non-empty labels
	// must be 1-63 characters long, and comply with [RFC1035]
	// (https://www.ietf.org/rfc/rfc1035.txt).
	// Specifically, the name must be 1-63 characters long and match the regular
	// expression `[a-z]([-a-z0-9]*[a-z0-9])?` which means the first
	// character must be a lowercase letter, and all following characters must be
	// a dash, lowercase letter, or digit, except the last character, which cannot
	// be a dash.
	Labels map[string]string `` /* 132-byte string literal not displayed */
}

The pipeline run arguments.

func (*RunPipelineArgs) Descriptor 

func (*RunPipelineArgs) Descriptor() ([]byte, []int)

func (*RunPipelineArgs) GetClientId 

func (m *RunPipelineArgs) GetClientId() string

func (*RunPipelineArgs) GetInputs 

func (m *RunPipelineArgs) GetInputs() map[string]string

func (*RunPipelineArgs) GetKeepVmAliveOnFailureDuration 

func (m *RunPipelineArgs) GetKeepVmAliveOnFailureDuration() *google_protobuf3.Duration

func (*RunPipelineArgs) GetLabels 

func (m *RunPipelineArgs) GetLabels() map[string]string

func (*RunPipelineArgs) GetLogging 

func (m *RunPipelineArgs) GetLogging() *LoggingOptions

func (*RunPipelineArgs) GetOutputs 

func (m *RunPipelineArgs) GetOutputs() map[string]string

func (*RunPipelineArgs) GetProjectId 

func (m *RunPipelineArgs) GetProjectId() string

func (*RunPipelineArgs) GetResources 

func (m *RunPipelineArgs) GetResources() *PipelineResources

func (*RunPipelineArgs) GetServiceAccount 

func (m *RunPipelineArgs) GetServiceAccount() *ServiceAccount

func (*RunPipelineArgs) ProtoMessage 

func (*RunPipelineArgs) ProtoMessage()

func (*RunPipelineArgs) Reset 

func (m *RunPipelineArgs) Reset()

func (*RunPipelineArgs) String 

func (m *RunPipelineArgs) String() string

type RunPipelineRequest 

type RunPipelineRequest struct {
	// Types that are valid to be assigned to Pipeline:
	//	*RunPipelineRequest_PipelineId
	//	*RunPipelineRequest_EphemeralPipeline
	Pipeline isRunPipelineRequest_Pipeline `protobuf_oneof:"pipeline"`
	// The arguments to use when running this pipeline.
	PipelineArgs *RunPipelineArgs `protobuf:"bytes,3,opt,name=pipeline_args,json=pipelineArgs" json:"pipeline_args,omitempty"`
}

The request to run a pipeline. If `pipelineId` is specified, it refers to a saved pipeline created with CreatePipeline and set as the `pipelineId` of the returned Pipeline object. If `ephemeralPipeline` is specified, that pipeline is run once with the given args and not saved. It is an error to specify both `pipelineId` and `ephemeralPipeline`. `pipelineArgs` must be specified.

func (*RunPipelineRequest) Descriptor 

func (*RunPipelineRequest) Descriptor() ([]byte, []int)

func (*RunPipelineRequest) GetEphemeralPipeline 

func (m *RunPipelineRequest) GetEphemeralPipeline() *Pipeline

func (*RunPipelineRequest) GetPipeline 

func (m *RunPipelineRequest) GetPipeline() isRunPipelineRequest_Pipeline

func (*RunPipelineRequest) GetPipelineArgs 

func (m *RunPipelineRequest) GetPipelineArgs() *RunPipelineArgs

func (*RunPipelineRequest) GetPipelineId 

func (m *RunPipelineRequest) GetPipelineId() string

func (*RunPipelineRequest) ProtoMessage 

func (*RunPipelineRequest) ProtoMessage()

func (*RunPipelineRequest) Reset 

func (m *RunPipelineRequest) Reset()

func (*RunPipelineRequest) String 

func (m *RunPipelineRequest) String() string

func (*RunPipelineRequest) XXX_OneofFuncs 

func (*RunPipelineRequest) XXX_OneofFuncs() (func(msg proto.Message, b *proto.Buffer) error, func(msg proto.Message, tag, wire int, b *proto.Buffer) (bool, error), func(msg proto.Message) (n int), []interface{})

XXX_OneofFuncs is for the internal use of the proto package.

type RunPipelineRequest_EphemeralPipeline 

type RunPipelineRequest_EphemeralPipeline struct {
	EphemeralPipeline *Pipeline `protobuf:"bytes,2,opt,name=ephemeral_pipeline,json=ephemeralPipeline,oneof"`
}

type RunPipelineRequest_PipelineId 

type RunPipelineRequest_PipelineId struct {
	PipelineId string `protobuf:"bytes,1,opt,name=pipeline_id,json=pipelineId,oneof"`
}

type RuntimeMetadata 

type RuntimeMetadata struct {
	// Execution information specific to Google Compute Engine.
	ComputeEngine *ComputeEngine `protobuf:"bytes,1,opt,name=compute_engine,json=computeEngine" json:"compute_engine,omitempty"`
}

Runtime metadata that will be populated in the [runtimeMetadata][google.genomics.v1.OperationMetadata.runtime_metadata] field of the Operation associated with a RunPipeline execution.

func (*RuntimeMetadata) Descriptor 

func (*RuntimeMetadata) Descriptor() ([]byte, []int)

func (*RuntimeMetadata) GetComputeEngine 

func (m *RuntimeMetadata) GetComputeEngine() *ComputeEngine

func (*RuntimeMetadata) ProtoMessage 

func (*RuntimeMetadata) ProtoMessage()

func (*RuntimeMetadata) Reset 

func (m *RuntimeMetadata) Reset()

func (*RuntimeMetadata) String 

func (m *RuntimeMetadata) String() string

type ServiceAccount 

type ServiceAccount struct {
	// Email address of the service account. Defaults to `default`,
	// which uses the compute service account associated with the project.
	Email string `protobuf:"bytes,1,opt,name=email" json:"email,omitempty"`
	// List of scopes to be enabled for this service account on the VM.
	// The following scopes are automatically included:
	//
	// * https://www.googleapis.com/auth/compute
	// * https://www.googleapis.com/auth/devstorage.full_control
	// * https://www.googleapis.com/auth/genomics
	// * https://www.googleapis.com/auth/logging.write
	// * https://www.googleapis.com/auth/monitoring.write
	Scopes []string `protobuf:"bytes,2,rep,name=scopes" json:"scopes,omitempty"`
}

A Google Cloud Service Account.

func (*ServiceAccount) Descriptor 

func (*ServiceAccount) Descriptor() ([]byte, []int)

func (*ServiceAccount) GetEmail 

func (m *ServiceAccount) GetEmail() string

func (*ServiceAccount) GetScopes 

func (m *ServiceAccount) GetScopes() []string

func (*ServiceAccount) ProtoMessage 

func (*ServiceAccount) ProtoMessage()

func (*ServiceAccount) Reset 

func (m *ServiceAccount) Reset()

func (*ServiceAccount) String 

func (m *ServiceAccount) String() string

type SetOperationStatusRequest 

type SetOperationStatusRequest struct {
	OperationId     string            `protobuf:"bytes,1,opt,name=operation_id,json=operationId" json:"operation_id,omitempty"`
	TimestampEvents []*TimestampEvent `protobuf:"bytes,2,rep,name=timestamp_events,json=timestampEvents" json:"timestamp_events,omitempty"`
	ErrorCode       google_rpc1.Code  `protobuf:"varint,3,opt,name=error_code,json=errorCode,enum=google.rpc.Code" json:"error_code,omitempty"`
	ErrorMessage    string            `protobuf:"bytes,4,opt,name=error_message,json=errorMessage" json:"error_message,omitempty"`
	ValidationToken uint64            `protobuf:"varint,5,opt,name=validation_token,json=validationToken" json:"validation_token,omitempty"`
}

Request to set operation status. Should only be used by VMs created by the Pipelines Service and not by end users.

func (*SetOperationStatusRequest) Descriptor 

func (*SetOperationStatusRequest) Descriptor() ([]byte, []int)

func (*SetOperationStatusRequest) GetErrorCode 

func (m *SetOperationStatusRequest) GetErrorCode() google_rpc1.Code

func (*SetOperationStatusRequest) GetErrorMessage 

func (m *SetOperationStatusRequest) GetErrorMessage() string

func (*SetOperationStatusRequest) GetOperationId 

func (m *SetOperationStatusRequest) GetOperationId() string

func (*SetOperationStatusRequest) GetTimestampEvents 

func (m *SetOperationStatusRequest) GetTimestampEvents() []*TimestampEvent

func (*SetOperationStatusRequest) GetValidationToken 

func (m *SetOperationStatusRequest) GetValidationToken() uint64

func (*SetOperationStatusRequest) ProtoMessage 

func (*SetOperationStatusRequest) ProtoMessage()

func (*SetOperationStatusRequest) Reset 

func (m *SetOperationStatusRequest) Reset()

func (*SetOperationStatusRequest) String 

func (m *SetOperationStatusRequest) String() string

type TimestampEvent 

type TimestampEvent struct {
	// String indicating the type of event
	Description string `protobuf:"bytes,1,opt,name=description" json:"description,omitempty"`
	// The time this event occured.
	Timestamp *google_protobuf4.Timestamp `protobuf:"bytes,2,opt,name=timestamp" json:"timestamp,omitempty"`
}

Stores the list of events and times they occured for major events in job execution.

func (*TimestampEvent) Descriptor 

func (*TimestampEvent) Descriptor() ([]byte, []int)

func (*TimestampEvent) GetDescription 

func (m *TimestampEvent) GetDescription() string

func (*TimestampEvent) GetTimestamp 

func (m *TimestampEvent) GetTimestamp() *google_protobuf4.Timestamp

func (*TimestampEvent) ProtoMessage 

func (*TimestampEvent) ProtoMessage()

func (*TimestampEvent) Reset 

func (m *TimestampEvent) Reset()

func (*TimestampEvent) String 

func (m *TimestampEvent) String() string

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