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// Copyright 2016 Google Inc.
//
// 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.
syntax = "proto3";
package google.genomics.v1alpha2;
import "google/api/annotations.proto";
import "google/longrunning/operations.proto";
import "google/protobuf/duration.proto";
import "google/protobuf/empty.proto";
import "google/protobuf/timestamp.proto";
import "google/rpc/code.proto";
option cc_enable_arenas = true;
option go_package = "google.golang.org/genproto/googleapis/genomics/v1alpha2;genomics";
option java_multiple_files = true;
option java_outer_classname = "PipelinesProto";
option java_package = "com.google.genomics.v1a";
// A service for running genomics pipelines.
service PipelinesV1Alpha2 {
// 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.
rpc CreatePipeline(CreatePipelineRequest) returns (Pipeline) {
option (google.api.http) = { post: "/v1alpha2/pipelines" body: "pipeline" };
}
// 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.
rpc RunPipeline(RunPipelineRequest) returns (google.longrunning.Operation) {
option (google.api.http) = { post: "/v1alpha2/pipelines:run" body: "*" };
}
// Retrieves a pipeline based on ID.
//
// Caller must have READ permission to the project.
rpc GetPipeline(GetPipelineRequest) returns (Pipeline) {
option (google.api.http) = { get: "/v1alpha2/pipelines/{pipeline_id}" };
}
// Lists pipelines.
//
// Caller must have READ permission to the project.
rpc ListPipelines(ListPipelinesRequest) returns (ListPipelinesResponse) {
option (google.api.http) = { get: "/v1alpha2/pipelines" };
}
// Deletes a pipeline based on ID.
//
// Caller must have WRITE permission to the project.
rpc DeletePipeline(DeletePipelineRequest) returns (google.protobuf.Empty) {
option (google.api.http) = { delete: "/v1alpha2/pipelines/{pipeline_id}" };
}
// Gets controller configuration information. Should only be called
// by VMs created by the Pipelines Service and not by end users.
rpc GetControllerConfig(GetControllerConfigRequest) returns (ControllerConfig) {
option (google.api.http) = { get: "/v1alpha2/pipelines:getControllerConfig" };
}
// 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.
rpc SetOperationStatus(SetOperationStatusRequest) returns (google.protobuf.Empty) {
option (google.api.http) = { put: "/v1alpha2/pipelines:setOperationStatus" body: "*" };
}
}
// Describes a Compute Engine resource that is being managed by a running
// [pipeline][google.genomics.v1alpha2.Pipeline].
message ComputeEngine {
// The instance on which the operation is running.
string instance_name = 1;
// The availability zone in which the instance resides.
string zone = 2;
// The machine type of the instance.
string machine_type = 3;
// The names of the disks that were created for this pipeline.
repeated string disk_names = 4;
}
// Runtime metadata that will be populated in the
// [runtimeMetadata][google.genomics.v1.OperationMetadata.runtime_metadata]
// field of the Operation associated with a RunPipeline execution.
message RuntimeMetadata {
// Execution information specific to Google Compute Engine.
ComputeEngine compute_engine = 1;
}
// 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.
message Pipeline {
// Required. The project in which to create the pipeline. The caller must have
// WRITE access.
string project_id = 1;
// Required. A user specified pipeline name that does not have to be unique.
// This name can be used for filtering Pipelines in ListPipelines.
string name = 2;
// User-specified description.
string description = 3;
// Input parameters of the pipeline.
repeated PipelineParameter input_parameters = 8;
// Output parameters of the pipeline.
repeated PipelineParameter output_parameters = 9;
// Required. The executor indicates in which environment the pipeline runs.
oneof executor {
// Specifies the docker run information.
DockerExecutor docker = 5;
}
// 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]
PipelineResources resources = 6;
// 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.
string pipeline_id = 7;
}
// The request to create a pipeline. The pipeline field here should not have
// `pipelineId` populated, as that will be populated by the server.
message CreatePipelineRequest {
// The pipeline to create. Should not have `pipelineId` populated.
Pipeline pipeline = 1;
}
// The pipeline run arguments.
message RunPipelineArgs {
// 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.
string project_id = 1;
// 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.
map<string, string> inputs = 2;
// 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.
map<string, string> outputs = 3;
// 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 service_account = 4;
// This field is deprecated. Use `labels` instead. Client-specified pipeline
// operation identifier.
string client_id = 5;
// Specifies resource requirements/overrides for the pipeline run.
PipelineResources resources = 6;
// Required. Logging options. Used by the service to communicate results
// to the user.
LoggingOptions logging = 7;
// 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.
google.protobuf.Duration keep_vm_alive_on_failure_duration = 8;
// 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.
map<string, string> labels = 9;
}
// 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.
message RunPipelineRequest {
oneof pipeline {
// The already created pipeline to run.
string pipeline_id = 1;
// A new pipeline object to run once and then delete.
Pipeline ephemeral_pipeline = 2;
}
// The arguments to use when running this pipeline.
RunPipelineArgs pipeline_args = 3;
}
// A request to get a saved pipeline by id.
message GetPipelineRequest {
// Caller must have READ access to the project in which this pipeline
// is defined.
string pipeline_id = 1;
}
// 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.
message ListPipelinesRequest {
// Required. The name of the project to search for pipelines. Caller
// must have READ access to this project.
string project_id = 1;
// Pipelines with names that match this prefix should be
// returned. If unspecified, all pipelines in the project, up to
// `pageSize`, will be returned.
string name_prefix = 2;
// Number of pipelines to return at once. Defaults to 256, and max
// is 2048.
int32 page_size = 3;
// Token to use to indicate where to start getting results.
// If unspecified, returns the first page of results.
string page_token = 4;
}
// 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.
message ListPipelinesResponse {
// The matched pipelines.
repeated Pipeline pipelines = 1;
// The token to use to get the next page of results.
string next_page_token = 2;
}
// The request to delete a saved pipeline by ID.
message DeletePipelineRequest {
// Caller must have WRITE access to the project in which this pipeline
// is defined.
string pipeline_id = 1;
}
// Request to get controller configuation. Should only be used
// by VMs created by the Pipelines Service and not by end users.
message GetControllerConfigRequest {
// The operation to retrieve controller configuration for.
string operation_id = 1;
uint64 validation_token = 2;
}
// 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.
message ControllerConfig {
message RepeatedString {
repeated string values = 1;
}
string image = 1;
string cmd = 2;
string gcs_log_path = 3;
string machine_type = 4;
map<string, string> vars = 5;
map<string, string> disks = 6;
map<string, RepeatedString> gcs_sources = 7;
map<string, RepeatedString> gcs_sinks = 8;
}
// Stores the list of events and times they occured for major events in job
// execution.
message TimestampEvent {
// String indicating the type of event
string description = 1;
// The time this event occured.
google.protobuf.Timestamp timestamp = 2;
}
// Request to set operation status. Should only be used by VMs
// created by the Pipelines Service and not by end users.
message SetOperationStatusRequest {
string operation_id = 1;
repeated TimestampEvent timestamp_events = 2;
google.rpc.Code error_code = 3;
string error_message = 4;
uint64 validation_token = 5;
}
// A Google Cloud Service Account.
message ServiceAccount {
// Email address of the service account. Defaults to `default`,
// which uses the compute service account associated with the project.
string email = 1;
// 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
repeated string scopes = 2;
}
// The logging options for the pipeline run.
message LoggingOptions {
// 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`.
string gcs_path = 1;
}
// The system resources for the pipeline run.
message PipelineResources {
// A Google Compute Engine disk resource specification.
message Disk {
// The types of disks that may be attached to VMs.
enum Type {
// Default disk type. Use one of the other options below.
TYPE_UNSPECIFIED = 0;
// Specifies a Google Compute Engine persistent hard disk. See
// https://cloud.google.com/compute/docs/disks/#pdspecs for details.
PERSISTENT_HDD = 1;
// Specifies a Google Compute Engine persistent solid-state disk. See
// https://cloud.google.com/compute/docs/disks/#pdspecs for details.
PERSISTENT_SSD = 2;
// Specifies a Google Compute Engine local SSD.
// See https://cloud.google.com/compute/docs/disks/local-ssd for details.
LOCAL_SSD = 3;
}
// 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.
string name = 1;
// Required. The type of the disk to create.
Type type = 2;
// The size of the disk. Defaults to 500 (GB).
// This field is not applicable for local SSD.
int32 size_gb = 3;
// 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.
string source = 4;
// 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.
bool auto_delete = 6;
// 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`.
string mount_point = 8;
}
// The minimum number of cores to use. Defaults to 1.
int32 minimum_cpu_cores = 1;
// 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.
bool preemptible = 2;
// The minimum amount of RAM to use. Defaults to 3.75 (GB)
double minimum_ram_gb = 3;
// Disks to attach.
repeated Disk disks = 4;
// List of Google Compute Engine availability zones to which resource
// creation will restricted. If empty, any zone may be chosen.
repeated string zones = 5;
// The size of the boot disk. Defaults to 10 (GB).
int32 boot_disk_size_gb = 6;
// 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.**
bool no_address = 7;
}
// 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.
message PipelineParameter {
// LocalCopy defines how a remote file should be copied to and from the VM.
message LocalCopy {
// 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,
string path = 1;
// 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 `/`.
string disk = 2;
}
// Required. Name of the parameter - the pipeline runner uses this string
// as the key to the input and output maps in RunPipeline.
string name = 1;
// Human-readable description.
string description = 2;
// 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://`.
string default_value = 5;
// 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 local_copy = 6;
}
// The Docker execuctor specification.
message DockerExecutor {
// Required. Image name from either Docker Hub or Google Container Registry.
// Users that run pipelines must have READ access to the image.
string image_name = 1;
// 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.
string cmd = 2;
}