service

Documentation

Overview

Package service implements the Archer service API.

Index

• func GetAmpliconCoverage(sampleStats *api.SampleStats) (int, int, float64)
• func NewArcher(options ...ArcherOption) (api.ArcherServer, func() error, error)
• func NewSample(options ...SampleOption) (*api.SampleInfo, error)
• type Archer
  • func (a *Archer) Cancel(ctx context.Context, request *api.CancelRequest) (*api.CancelResponse, error)
  • func (a *Archer) Process(ctx context.Context, request *api.ProcessRequest) (*api.ProcessResponse, error)
  • func (a *Archer) Watch(request *api.WatchRequest, stream api.Archer_WatchServer) error
• type ArcherOption
  • func SetBucket(name, region string) ArcherOption
  • func SetDb(dbPath string) ArcherOption
  • func SetManifest(manifestURL string) ArcherOption
  • func SetNumWorkers(numWorkers int) ArcherOption
• type SampleOption
  • func SetID(id string) SampleOption
  • func SetRequest(request *api.ProcessRequest) SampleOption

Functions

func GetAmpliconCoverage

func GetAmpliconCoverage(sampleStats *api.SampleStats) (int, int, float64)

GetAmpliconCoverage will check SampleStats and return the number of covered amplicons, the total number of amplicons and the mean coverage.

func NewArcher

func NewArcher(options ...ArcherOption) (api.ArcherServer, func() error, error)

NewArcher creates the Archer server and returns it along with the shutdown method and any constructor error.

func NewSample

func NewSample(options ...SampleOption) (*api.SampleInfo, error)

NewSample will return an initialised SampleInfo struct with default values.

Types

type Archer

type Archer struct {

	// service lock
	sync.RWMutex
	// contains filtered or unexported fields
}

Archer is an implementation of the v1.ArcherServer.

It includes some extra data and methods to provide extra functionality.

func (*Archer) Cancel

func (a *Archer) Cancel(ctx context.Context, request *api.CancelRequest) (*api.CancelResponse, error)

Cancel is used to...

func (*Archer) Process

func (a *Archer) Process(ctx context.Context, request *api.ProcessRequest) (*api.ProcessResponse, error)

Process will begin processing for a sample.

func (*Archer) Watch

func (a *Archer) Watch(request *api.WatchRequest, stream api.Archer_WatchServer) error

Watch will respond to WatchRequests by streaming completed samples back to the user as they are marked done by Archer.

type ArcherOption

type ArcherOption func(archer *Archer) error

ArcherOption is a wrapper struct used to pass functional options to the Archer constructor.

func SetBucket

func SetBucket(name, region string) ArcherOption

SetBucket is an option setter for the NewArcher constructor that sets the S3 bucket field of the Archer struct.

func SetDb

func SetDb(dbPath string) ArcherOption

SetDb is an option setter for the NewArcher constructor that opens a db at the specified path and sets the appropriate field of the Archer struct.

func SetManifest

func SetManifest(manifestURL string) ArcherOption

SetManifest is an option setter for the NewArcher constructor that downloads and opens a manifest and sets the appropriate field of the Archer struct.

func SetNumWorkers

func SetNumWorkers(numWorkers int) ArcherOption

SetNumWorkers is an option setter for the NewArcher constructor that sets the number of concurrent process request workers to use.

type SampleOption

type SampleOption func(sample *api.SampleInfo) error

SampleOption is a wrapper struct used to pass functional options to the Sample constructor.

func SetID

func SetID(id string) SampleOption

SetID is an option setter for the NewSample constructor that sets the ID field of a SampleInfo struct.

func SetRequest

func SetRequest(request *api.ProcessRequest) SampleOption

SetRequest is an option setter for the NewSample constructor that sets the request field of a SampleInfo struct and populates some additional data.