Struct google_api_proto::google::genomics::v1alpha2::PipelineParameter

pub struct PipelineParameter {
    pub name: String,
    pub description: String,
    pub default_value: String,
    pub local_copy: Option<LocalCopy>,
}

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:

Google Cloud storage path	Local path
file	file
glob	directory

For outputs, the direction of the copy is reversed:

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

Acceptable paths are:

Local path	Google Cloud Storage path
file	file
file	directory - directory must already exist
glob	directory - directory will be created if it doesn't exist

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.

Fields

name: String

Required. Name of the parameter - the pipeline runner uses this string as the key to the input and output maps in RunPipeline.

description: String

Human-readable description.

default_value: String

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://.

local_copy: Option<LocalCopy>

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.

Trait Implementations

impl Clone for PipelineParameter

fn clone(&self) -> PipelineParameter

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for PipelineParameter

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for PipelineParameter

fn default() -> Self

Returns the “default value” for a type.

impl Message for PipelineParameter

fn encoded_len(&self) -> usize

Returns the encoded length of the message without a length delimiter.

fn clear(&mut self)

Clears the message, resetting all fields to their default.

fn encode<B>(&self, buf: &mut B) -> Result<(), EncodeError>

where B: BufMut, Self: Sized,

Encodes the message to a buffer.

fn encode_to_vec(&self) -> Vec<u8>

where Self: Sized,

Encodes the message to a newly allocated buffer.

fn encode_length_delimited<B>(&self, buf: &mut B) -> Result<(), EncodeError>

where B: BufMut, Self: Sized,

Encodes the message with a length-delimiter to a buffer.

fn encode_length_delimited_to_vec(&self) -> Vec<u8>

where Self: Sized,

Encodes the message with a length-delimiter to a newly allocated buffer.

fn decode<B>(buf: B) -> Result<Self, DecodeError>

where B: Buf, Self: Default,

Decodes an instance of the message from a buffer.

fn decode_length_delimited<B>(buf: B) -> Result<Self, DecodeError>

where B: Buf, Self: Default,

Decodes a length-delimited instance of the message from the buffer.

fn merge<B>(&mut self, buf: B) -> Result<(), DecodeError>

where B: Buf, Self: Sized,

Decodes an instance of the message from a buffer, and merges it into self.

fn merge_length_delimited<B>(&mut self, buf: B) -> Result<(), DecodeError>

where B: Buf, Self: Sized,

Decodes a length-delimited instance of the message from buffer, and merges it into self.

impl PartialEq for PipelineParameter

fn eq(&self, other: &PipelineParameter) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl StructuralPartialEq for PipelineParameter