v1

package
v0.1.1 Latest Latest
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 Go to latest Published: Apr 7, 2021 License: MIT Imports: 10 Imported by: 2

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Index

Constants

This section is empty.

Variables

View Source 
var (
	State_name = map[int32]string{
		0: "UNKNOWN",
		1: "RUNNING",
		2: "SUCCESS",
		3: "ERROR",
		4: "CANCELLED",
	}
	State_value = map[string]int32{
		"UNKNOWN":   0,
		"RUNNING":   1,
		"SUCCESS":   2,
		"ERROR":     3,
		"CANCELLED": 4,
	}
)

Enum value maps for State.

View Source 
var File_api_proto_v1_archer_proto protoreflect.FileDescriptor
View Source 
var File_api_proto_v1_schemes_proto protoreflect.FileDescriptor

Functions

func RegisterArcherServer 

func RegisterArcherServer(s *grpc.Server, srv ArcherServer)

Types

type ArcherClient 

type ArcherClient interface {
	// Process will begin processing for a sample.
	Process(ctx context.Context, in *ProcessRequest, opts ...grpc.CallOption) (*ProcessResponse, error)
	// Cancel will cancel processing for a sample.
	Cancel(ctx context.Context, in *CancelRequest, opts ...grpc.CallOption) (*CancelResponse, error)
	// Watch sample processing, returning messages when sample processing starts, stops or updates
	// The current state of all currently-processing samples will be returned in the initial set
	// of messages, with the option of also including finished samples.
	Watch(ctx context.Context, in *WatchRequest, opts ...grpc.CallOption) (Archer_WatchClient, error)
}

ArcherClient is the client API for Archer service.

For semantics around ctx use and closing/ending streaming RPCs, please refer to https://godoc.org/google.golang.org/grpc#ClientConn.NewStream.

func NewArcherClient 

func NewArcherClient(cc grpc.ClientConnInterface) ArcherClient

type ArcherServer 

type ArcherServer interface {
	// Process will begin processing for a sample.
	Process(context.Context, *ProcessRequest) (*ProcessResponse, error)
	// Cancel will cancel processing for a sample.
	Cancel(context.Context, *CancelRequest) (*CancelResponse, error)
	// Watch sample processing, returning messages when sample processing starts, stops or updates
	// The current state of all currently-processing samples will be returned in the initial set
	// of messages, with the option of also including finished samples.
	Watch(*WatchRequest, Archer_WatchServer) error
}

ArcherServer is the server API for Archer service.

type Archer_WatchClient 

type Archer_WatchClient interface {
	Recv() (*WatchResponse, error)
	grpc.ClientStream
}

type Archer_WatchServer 

type Archer_WatchServer interface {
	Send(*WatchResponse) error
	grpc.ServerStream
}

type CancelRequest 

type CancelRequest struct {

	// api version
	ApiVersion string `protobuf:"bytes,1,opt,name=apiVersion,proto3" json:"apiVersion,omitempty"`
	// identifier for the sample
	Id string `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
	// contains filtered or unexported fields
}

CancelRequest will cancel processing for a sample.

func (*CancelRequest) Descriptor deprecated 

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

Deprecated: Use CancelRequest.ProtoReflect.Descriptor instead.

func (*CancelRequest) GetApiVersion 

func (x *CancelRequest) GetApiVersion() string

func (*CancelRequest) GetId 

func (x *CancelRequest) GetId() string

func (*CancelRequest) ProtoMessage 

func (*CancelRequest) ProtoMessage()

func (*CancelRequest) ProtoReflect 

func (x *CancelRequest) ProtoReflect() protoreflect.Message

func (*CancelRequest) Reset 

func (x *CancelRequest) Reset()

func (*CancelRequest) String 

func (x *CancelRequest) String() string

type CancelResponse 

type CancelResponse struct {
	// contains filtered or unexported fields
}

CancelResponse.

func (*CancelResponse) Descriptor deprecated 

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

Deprecated: Use CancelResponse.ProtoReflect.Descriptor instead.

func (*CancelResponse) ProtoMessage 

func (*CancelResponse) ProtoMessage()

func (*CancelResponse) ProtoReflect 

func (x *CancelResponse) ProtoReflect() protoreflect.Message

func (*CancelResponse) Reset 

func (x *CancelResponse) Reset()

func (*CancelResponse) String 

func (x *CancelResponse) String() string

type Manifest 

type Manifest struct {
	Metadata   string                     `protobuf:"bytes,1,opt,name=metadata,proto3" json:"metadata,omitempty"`
	Repository string                     `protobuf:"bytes,2,opt,name=repository,proto3" json:"repository,omitempty"`
	LatestDoi  string                     `protobuf:"bytes,3,opt,name=latest_doi,json=latestDoi,proto3" json:"latest_doi,omitempty"`
	License    string                     `protobuf:"bytes,4,opt,name=license,proto3" json:"license,omitempty"`
	Schemes    map[string]*SchemeMetadata `` /* 155-byte string literal not displayed */
	// contains filtered or unexported fields
}

Manifest represents the structure used by ARTIC to store scheme metadata.

func (*Manifest) Descriptor deprecated 

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

Deprecated: Use Manifest.ProtoReflect.Descriptor instead.

func (*Manifest) GetLatestDoi 

func (x *Manifest) GetLatestDoi() string

func (*Manifest) GetLicense 

func (x *Manifest) GetLicense() string

func (*Manifest) GetMetadata 

func (x *Manifest) GetMetadata() string

func (*Manifest) GetRepository 

func (x *Manifest) GetRepository() string

func (*Manifest) GetSchemes 

func (x *Manifest) GetSchemes() map[string]*SchemeMetadata

func (*Manifest) ProtoMessage 

func (*Manifest) ProtoMessage()

func (*Manifest) ProtoReflect 

func (x *Manifest) ProtoReflect() protoreflect.Message

func (*Manifest) Reset 

func (x *Manifest) Reset()

func (*Manifest) String 

func (x *Manifest) String() string

type ProcessRequest 

type ProcessRequest struct {

	// api version
	ApiVersion string `protobuf:"bytes,1,opt,name=apiVersion,proto3" json:"apiVersion,omitempty"`
	// sampleID is the sample identifier - users job to assign this and make it unique
	SampleID string `protobuf:"bytes,2,opt,name=sampleID,proto3" json:"sampleID,omitempty"`
	// inputFASTQfiles for this sample
	InputFASTQfiles []string `protobuf:"bytes,3,rep,name=inputFASTQfiles,proto3" json:"inputFASTQfiles,omitempty"`
	// scheme denotes the amplicon scheme used for the sample
	Scheme string `protobuf:"bytes,4,opt,name=scheme,proto3" json:"scheme,omitempty"`
	// schemeVersion denotes the amplicon scheme version used
	SchemeVersion int32 `protobuf:"varint,5,opt,name=schemeVersion,proto3" json:"schemeVersion,omitempty"`
	// contains filtered or unexported fields
}

ProcessRequest will request a sample to be processed by Archer.

func (*ProcessRequest) Descriptor deprecated 

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

Deprecated: Use ProcessRequest.ProtoReflect.Descriptor instead.

func (*ProcessRequest) GetApiVersion 

func (x *ProcessRequest) GetApiVersion() string

func (*ProcessRequest) GetInputFASTQfiles 

func (x *ProcessRequest) GetInputFASTQfiles() []string

func (*ProcessRequest) GetSampleID 

func (x *ProcessRequest) GetSampleID() string

func (*ProcessRequest) GetScheme 

func (x *ProcessRequest) GetScheme() string

func (*ProcessRequest) GetSchemeVersion 

func (x *ProcessRequest) GetSchemeVersion() int32

func (*ProcessRequest) ProtoMessage 

func (*ProcessRequest) ProtoMessage()

func (*ProcessRequest) ProtoReflect 

func (x *ProcessRequest) ProtoReflect() protoreflect.Message

func (*ProcessRequest) Reset 

func (x *ProcessRequest) Reset()

func (*ProcessRequest) String 

func (x *ProcessRequest) String() string

type ProcessResponse 

type ProcessResponse struct {

	// api version
	ApiVersion string `protobuf:"bytes,1,opt,name=apiVersion,proto3" json:"apiVersion,omitempty"`
	// identifier for the sample that processing was started for (used to monitor or cancel the sample)
	Id string `protobuf:"bytes,2,opt,name=id,proto3" json:"id,omitempty"`
	// contains filtered or unexported fields
}

ProcessResponse

func (*ProcessResponse) Descriptor deprecated 

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

Deprecated: Use ProcessResponse.ProtoReflect.Descriptor instead.

func (*ProcessResponse) GetApiVersion 

func (x *ProcessResponse) GetApiVersion() string

func (*ProcessResponse) GetId 

func (x *ProcessResponse) GetId() string

func (*ProcessResponse) ProtoMessage 

func (*ProcessResponse) ProtoMessage()

func (*ProcessResponse) ProtoReflect 

func (x *ProcessResponse) ProtoReflect() protoreflect.Message

func (*ProcessResponse) Reset 

func (x *ProcessResponse) Reset()

func (*ProcessResponse) String 

func (x *ProcessResponse) String() string

type SampleInfo 

type SampleInfo struct {

	// sampleID is the sample identifier - as returned by Process()
	SampleID string `protobuf:"bytes,1,opt,name=sampleID,proto3" json:"sampleID,omitempty"`
	// the original message used to start the sample processing
	ProcessRequest *ProcessRequest `protobuf:"bytes,2,opt,name=processRequest,proto3" json:"processRequest,omitempty"`
	// state the sample is in
	State State `protobuf:"varint,3,opt,name=state,proto3,enum=v1.State" json:"state,omitempty"`
	// errors will contain encountered errors (if state is STATE_ERROR, otherwise this will be empty)
	Errors []string `protobuf:"bytes,4,rep,name=errors,proto3" json:"errors,omitempty"`
	// filesDiscovered is the number of files found for this sample
	FilesDiscovered int32 `protobuf:"varint,5,opt,name=filesDiscovered,proto3" json:"filesDiscovered,omitempty"`
	// startTime for processing
	StartTime *timestamp.Timestamp `protobuf:"bytes,6,opt,name=startTime,proto3" json:"startTime,omitempty"`
	// endTime for processing (unset if processing still running)
	EndTime *timestamp.Timestamp `protobuf:"bytes,7,opt,name=endTime,proto3" json:"endTime,omitempty"`
	// processStats contains details on the processing request output
	ProcessStats *SampleStats `protobuf:"bytes,8,opt,name=processStats,proto3" json:"processStats,omitempty"`
	// endpoint is the AWS S3 location for the processed sample
	Endpoint string `protobuf:"bytes,9,opt,name=endpoint,proto3" json:"endpoint,omitempty"`
	// contains filtered or unexported fields
}

SampleInfo describes how a sample was processed by Archer.

func (*SampleInfo) Descriptor deprecated 

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

Deprecated: Use SampleInfo.ProtoReflect.Descriptor instead.

func (*SampleInfo) GetEndTime 

func (x *SampleInfo) GetEndTime() *timestamp.Timestamp

func (*SampleInfo) GetEndpoint 

func (x *SampleInfo) GetEndpoint() string

func (*SampleInfo) GetErrors 

func (x *SampleInfo) GetErrors() []string

func (*SampleInfo) GetFilesDiscovered 

func (x *SampleInfo) GetFilesDiscovered() int32

func (*SampleInfo) GetProcessRequest 

func (x *SampleInfo) GetProcessRequest() *ProcessRequest

func (*SampleInfo) GetProcessStats 

func (x *SampleInfo) GetProcessStats() *SampleStats

func (*SampleInfo) GetSampleID 

func (x *SampleInfo) GetSampleID() string

func (*SampleInfo) GetStartTime 

func (x *SampleInfo) GetStartTime() *timestamp.Timestamp

func (*SampleInfo) GetState 

func (x *SampleInfo) GetState() State

func (*SampleInfo) ProtoMessage 

func (*SampleInfo) ProtoMessage()

func (*SampleInfo) ProtoReflect 

func (x *SampleInfo) ProtoReflect() protoreflect.Message

func (*SampleInfo) Reset 

func (x *SampleInfo) Reset()

func (*SampleInfo) String 

func (x *SampleInfo) String() string

type SampleStats 

type SampleStats struct {

	// total reads across all FASTQs for a sample
	TotalReads int32 `protobuf:"varint,1,opt,name=totalReads,proto3" json:"totalReads,omitempty"`
	// kept reads across all FASTQs for a sample
	KeptReads int32 `protobuf:"varint,2,opt,name=keptReads,proto3" json:"keptReads,omitempty"`
	// ampliconCoverage counts the numer of reads assigned to each amplicon for a sample
	AmpliconCoverage map[string]int32 `` /* 174-byte string literal not displayed */
	// meanAmpliconSize is the mean size of the reference amplicons (incl. primers)
	MeanAmpliconSize int32 `protobuf:"varint,4,opt,name=meanAmpliconSize,proto3" json:"meanAmpliconSize,omitempty"`
	// lengthMax is the maximum length allowed for a read to be kept.
	LengthMax int32 `protobuf:"varint,5,opt,name=lengthMax,proto3" json:"lengthMax,omitempty"`
	// minLength is the minimum length allowed for a read to be kept.
	LengthMin int32 `protobuf:"varint,6,opt,name=lengthMin,proto3" json:"lengthMin,omitempty"`
	// contains filtered or unexported fields
}

SampleStats stores basic numbers from the sample processing.

func (*SampleStats) Descriptor deprecated 

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

Deprecated: Use SampleStats.ProtoReflect.Descriptor instead.

func (*SampleStats) GetAmpliconCoverage 

func (x *SampleStats) GetAmpliconCoverage() map[string]int32

func (*SampleStats) GetKeptReads 

func (x *SampleStats) GetKeptReads() int32

func (*SampleStats) GetLengthMax 

func (x *SampleStats) GetLengthMax() int32

func (*SampleStats) GetLengthMin 

func (x *SampleStats) GetLengthMin() int32

func (*SampleStats) GetMeanAmpliconSize 

func (x *SampleStats) GetMeanAmpliconSize() int32

func (*SampleStats) GetTotalReads 

func (x *SampleStats) GetTotalReads() int32

func (*SampleStats) ProtoMessage 

func (*SampleStats) ProtoMessage()

func (*SampleStats) ProtoReflect 

func (x *SampleStats) ProtoReflect() protoreflect.Message

func (*SampleStats) Reset 

func (x *SampleStats) Reset()

func (*SampleStats) String 

func (x *SampleStats) String() string

type SchemeMetadata 

type SchemeMetadata struct {
	Aliases                  []string          `protobuf:"bytes,1,rep,name=aliases,proto3" json:"aliases,omitempty"`
	LatestVersion            int32             `protobuf:"varint,2,opt,name=latest_version,json=latestVersion,proto3" json:"latest_version,omitempty"`
	PrimerUrls               map[string]string `` /* 179-byte string literal not displayed */
	ReferenceUrls            map[string]string `` /* 188-byte string literal not displayed */
	PrimerSha256Checksums    map[string]string `` /* 214-byte string literal not displayed */
	ReferenceSha256Checksums map[string]string `` /* 223-byte string literal not displayed */
	// contains filtered or unexported fields
}

SchemeMetadata.

func (*SchemeMetadata) Descriptor deprecated 

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

Deprecated: Use SchemeMetadata.ProtoReflect.Descriptor instead.

func (*SchemeMetadata) GetAliases 

func (x *SchemeMetadata) GetAliases() []string

func (*SchemeMetadata) GetLatestVersion 

func (x *SchemeMetadata) GetLatestVersion() int32

func (*SchemeMetadata) GetPrimerSha256Checksums 

func (x *SchemeMetadata) GetPrimerSha256Checksums() map[string]string

func (*SchemeMetadata) GetPrimerUrls 

func (x *SchemeMetadata) GetPrimerUrls() map[string]string

func (*SchemeMetadata) GetReferenceSha256Checksums 

func (x *SchemeMetadata) GetReferenceSha256Checksums() map[string]string

func (*SchemeMetadata) GetReferenceUrls 

func (x *SchemeMetadata) GetReferenceUrls() map[string]string

func (*SchemeMetadata) ProtoMessage 

func (*SchemeMetadata) ProtoMessage()

func (*SchemeMetadata) ProtoReflect 

func (x *SchemeMetadata) ProtoReflect() protoreflect.Message

func (*SchemeMetadata) Reset 

func (x *SchemeMetadata) Reset()

func (*SchemeMetadata) String 

func (x *SchemeMetadata) String() string

type State 

type State int32

State of a sample being handled by Archer. 

const (
	// sample is queued
	State_UNKNOWN State = 0
	// sample prep is running
	State_RUNNING State = 1
	// sample prep is complete with no errors
	State_SUCCESS State = 2
	// sample prep has stopped due to errors
	State_ERROR State = 3
	// sample prep was cancelled via a call to cancel()
	State_CANCELLED State = 4
)

func (State) Descriptor 

func (State) Descriptor() protoreflect.EnumDescriptor

func (State) Enum 

func (x State) Enum() *State

func (State) EnumDescriptor deprecated 

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

Deprecated: Use State.Descriptor instead.

func (State) Number 

func (x State) Number() protoreflect.EnumNumber

func (State) String 

func (x State) String() string

func (State) Type 

func (State) Type() protoreflect.EnumType

type UnimplementedArcherServer 

type UnimplementedArcherServer struct {
}

UnimplementedArcherServer can be embedded to have forward compatible implementations.

func (*UnimplementedArcherServer) Cancel 

func (*UnimplementedArcherServer) Cancel(context.Context, *CancelRequest) (*CancelResponse, error)

func (*UnimplementedArcherServer) Process 

func (*UnimplementedArcherServer) Process(context.Context, *ProcessRequest) (*ProcessResponse, error)

func (*UnimplementedArcherServer) Watch 

func (*UnimplementedArcherServer) Watch(*WatchRequest, Archer_WatchServer) error

type WatchRequest 

type WatchRequest struct {

	// api version
	ApiVersion string `protobuf:"bytes,1,opt,name=apiVersion,proto3" json:"apiVersion,omitempty"`
	// sendFinished will tell Archer to also send information on samples that have completed procesing
	SendFinished bool `protobuf:"varint,2,opt,name=sendFinished,proto3" json:"sendFinished,omitempty"`
	// contains filtered or unexported fields
}

WatchRequest to monitor sample processing.

func (*WatchRequest) Descriptor deprecated 

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

Deprecated: Use WatchRequest.ProtoReflect.Descriptor instead.

func (*WatchRequest) GetApiVersion 

func (x *WatchRequest) GetApiVersion() string

func (*WatchRequest) GetSendFinished 

func (x *WatchRequest) GetSendFinished() bool

func (*WatchRequest) ProtoMessage 

func (*WatchRequest) ProtoMessage()

func (*WatchRequest) ProtoReflect 

func (x *WatchRequest) ProtoReflect() protoreflect.Message

func (*WatchRequest) Reset 

func (x *WatchRequest) Reset()

func (*WatchRequest) String 

func (x *WatchRequest) String() string

type WatchResponse 

type WatchResponse struct {

	// api version
	ApiVersion string `protobuf:"bytes,1,opt,name=apiVersion,proto3" json:"apiVersion,omitempty"`
	// current state of samples
	Samples []*SampleInfo `protobuf:"bytes,2,rep,name=samples,proto3" json:"samples,omitempty"`
	// contains filtered or unexported fields
}

WatchResponse.

func (*WatchResponse) Descriptor deprecated 

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

Deprecated: Use WatchResponse.ProtoReflect.Descriptor instead.

func (*WatchResponse) GetApiVersion 

func (x *WatchResponse) GetApiVersion() string

func (*WatchResponse) GetSamples 

func (x *WatchResponse) GetSamples() []*SampleInfo

func (*WatchResponse) ProtoMessage 

func (*WatchResponse) ProtoMessage()

func (*WatchResponse) ProtoReflect 

func (x *WatchResponse) ProtoReflect() protoreflect.Message

func (*WatchResponse) Reset 

func (x *WatchResponse) Reset()

func (*WatchResponse) String 

func (x *WatchResponse) String() string

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