records

package
v0.0.0-...-412bf38 Latest Latest
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 Go to latest Published: Aug 17, 2021 License: MIT Imports: 10 Imported by: 0

Documentation

Index

Constants

This section is empty.

Variables

View Source 
var (
	Status_name = map[int32]string{
		0: "UN_INITIALIZED",
		1: "untagged",
		2: "tagsIncomplete",
		3: "tagsComplete",
		4: "announced",
	}
	Status_value = map[string]int32{
		"UN_INITIALIZED": 0,
		"untagged":       1,
		"tagsIncomplete": 2,
		"tagsComplete":   3,
		"announced":      4,
	}
)

Enum value maps for Status.

View Source 
var (
	RecordType_name = map[int32]string{
		0: "run",
		1: "sample",
	}
	RecordType_value = map[string]int32{
		"run":    0,
		"sample": 1,
	}
)

Enum value maps for RecordType.

View Source 
var DefaultFastqExtensions []string = []string{"*.fastq", "*.fq"}

DefaultFastqExtensions is used to glob the files from directories

View Source 
var File_herald_records_proto protoreflect.FileDescriptor

Functions

This section is empty.

Types

type Comment 

type Comment struct {
	Timestamp *timestamp.Timestamp `protobuf:"bytes,1,opt,name=timestamp,proto3" json:"timestamp,omitempty"`
	Text      string               `protobuf:"bytes,2,opt,name=text,proto3" json:"text,omitempty"`
	// contains filtered or unexported fields
}

Comments are used to record generic text entries and to track the history of HeraldData.

func (*Comment) Descriptor deprecated 

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

Deprecated: Use Comment.ProtoReflect.Descriptor instead.

func (*Comment) GetText 

func (x *Comment) GetText() string

func (*Comment) GetTimestamp 

func (x *Comment) GetTimestamp() *timestamp.Timestamp

func (*Comment) ProtoMessage 

func (*Comment) ProtoMessage()

func (*Comment) ProtoReflect 

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

func (*Comment) Reset 

func (x *Comment) Reset()

func (*Comment) String 

func (x *Comment) String() string

type HeraldData 

type HeraldData struct {
	Created *timestamp.Timestamp `protobuf:"bytes,1,opt,name=created,proto3" json:"created,omitempty"`
	Label   string               `protobuf:"bytes,3,opt,name=label,proto3" json:"label,omitempty"`                        // the run or sample name
	History []*Comment           `protobuf:"bytes,4,rep,name=history,proto3" json:"history,omitempty"`                    // describes the history of the run
	Status  Status               `protobuf:"varint,5,opt,name=status,proto3,enum=records.Status" json:"status,omitempty"` // describes if untagged, tagged with complete/incomplete services and if announced
	Tags    map[string]bool      ``                                                                                       // tagged services and their complete status (true=complete, false=incomplete)
	/* 150-byte string literal not displayed */
	RequestOrder []string `protobuf:"bytes,7,rep,name=requestOrder,proto3" json:"requestOrder,omitempty"` // the order to send requests to the tagged services
	// contains filtered or unexported fields
}

HeraldData is the base data type. It is used by both Run and Sample.

func (*HeraldData) AddComment 

func (heraldData *HeraldData) AddComment(text string) error

AddComment is a method to add a comment to the history of an run or sample

func (*HeraldData) AddTags 

func (heraldData *HeraldData) AddTags(tags []string) error

AddTags is a method to tag a run or sample with a service

func (*HeraldData) CheckStatus 

func (heraldData *HeraldData) CheckStatus() error

CheckStatus checks the tags and updates the status if all tags are now marked complete TODO: this func is incomplete - it only checks for tagged services atm

func (*HeraldData) Descriptor deprecated 

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

Deprecated: Use HeraldData.ProtoReflect.Descriptor instead.

func (*HeraldData) GetCreated 

func (x *HeraldData) GetCreated() *timestamp.Timestamp

func (*HeraldData) GetHistory 

func (x *HeraldData) GetHistory() []*Comment

func (*HeraldData) GetLabel 

func (x *HeraldData) GetLabel() string

func (*HeraldData) GetRequestOrder 

func (x *HeraldData) GetRequestOrder() []string

func (*HeraldData) GetStatus 

func (x *HeraldData) GetStatus() Status

func (*HeraldData) GetTags 

func (x *HeraldData) GetTags() map[string]bool

func (*HeraldData) ProtoMessage 

func (*HeraldData) ProtoMessage()

func (*HeraldData) ProtoReflect 

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

func (*HeraldData) Reset 

func (x *HeraldData) Reset()

func (*HeraldData) SetStatus 

func (heraldData *HeraldData) SetStatus(status Status) error

SetStatus updates the status. TODO: do this better.

func (*HeraldData) SetTag 

func (heraldData *HeraldData) SetTag(serviceName string, value bool) error

SetTag is a method to set a tag either true or false (complete or incomplete)

func (*HeraldData) String 

func (x *HeraldData) String() string

type RecordType 

type RecordType int32

RecordType is used for differentiating between Herald Record types. 

const (
	RecordType_run    RecordType = 0
	RecordType_sample RecordType = 1
)

func (RecordType) Descriptor 

func (RecordType) Descriptor() protoreflect.EnumDescriptor

func (RecordType) Enum 

func (x RecordType) Enum() *RecordType

func (RecordType) EnumDescriptor deprecated 

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

Deprecated: Use RecordType.Descriptor instead.

func (RecordType) Number 

func (x RecordType) Number() protoreflect.EnumNumber

func (RecordType) String 

func (x RecordType) String() string

func (RecordType) Type 

func (RecordType) Type() protoreflect.EnumType

type Run 

type Run struct {
	Metadata             *HeraldData `protobuf:"bytes,1,opt,name=metadata,proto3" json:"metadata,omitempty"`
	OutputDirectory      string      `protobuf:"bytes,2,opt,name=outputDirectory,proto3" json:"outputDirectory,omitempty"`           // where the run is stored
	Fast5OutputDirectory string      `protobuf:"bytes,3,opt,name=fast5OutputDirectory,proto3" json:"fast5OutputDirectory,omitempty"` // where the run fast5 data is stored
	FastqOutputDirectory string      `protobuf:"bytes,4,opt,name=fastqOutputDirectory,proto3" json:"fastqOutputDirectory,omitempty"` // where the run fastq data is stored
	PrimerScheme         string      `protobuf:"bytes,5,opt,name=primerScheme,proto3" json:"primerScheme,omitempty"`                 // the ARTIC primer scheme name for this run
	// contains filtered or unexported fields
}

Run is used to describe a Nanopore sequencing run.

func InitRun 

func InitRun(label, outputDir, fast5Dir, fastqDir, primerScheme string) *Run

InitRun will init a run struct with the minimum required values

func (*Run) Descriptor deprecated 

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

Deprecated: Use Run.ProtoReflect.Descriptor instead.

func (*Run) GetFast5OutputDirectory 

func (x *Run) GetFast5OutputDirectory() string

func (*Run) GetFastqFiles 

func (r *Run) GetFastqFiles() ([]string, error)

GetFastqFiles will return a list of all fastq files found in the Run FASTQ directory.

func (*Run) GetFastqOutputDirectory 

func (x *Run) GetFastqOutputDirectory() string

func (*Run) GetMetadata 

func (x *Run) GetMetadata() *HeraldData

func (*Run) GetOutputDirectory 

func (x *Run) GetOutputDirectory() string

func (*Run) GetPrimerScheme 

func (x *Run) GetPrimerScheme() string

func (*Run) ProtoMessage 

func (*Run) ProtoMessage()

func (*Run) ProtoReflect 

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

func (*Run) Reset 

func (x *Run) Reset()

func (*Run) String 

func (x *Run) String() string

type Sample 

type Sample struct {
	Metadata  *HeraldData `protobuf:"bytes,1,opt,name=metadata,proto3" json:"metadata,omitempty"`
	ParentRun string      `protobuf:"bytes,2,opt,name=parentRun,proto3" json:"parentRun,omitempty"` // the label of the parent run, used to perform lookups
	Barcode   int32       `protobuf:"varint,3,opt,name=barcode,proto3" json:"barcode,omitempty"`
	// contains filtered or unexported fields
}

Sample is used to describe a biological sample which is being sequenced as part of a Run.

func InitSample 

func InitSample(sampleLabel, runLabel string, barcode int32) *Sample

InitSample will init a sample struct with the minimum required values

func (*Sample) Descriptor deprecated 

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

Deprecated: Use Sample.ProtoReflect.Descriptor instead.

func (*Sample) GetBarcode 

func (x *Sample) GetBarcode() int32

func (*Sample) GetMetadata 

func (x *Sample) GetMetadata() *HeraldData

func (*Sample) GetParentRun 

func (x *Sample) GetParentRun() string

func (*Sample) ProtoMessage 

func (*Sample) ProtoMessage()

func (*Sample) ProtoReflect 

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

func (*Sample) Reset 

func (x *Sample) Reset()

func (*Sample) String 

func (x *Sample) String() string

type Status 

type Status int32

Status is used to determine if runs/samples have tagged service requests and if they have been announced via the message server. 

const (
	Status_UN_INITIALIZED Status = 0
	Status_untagged       Status = 1 // data is not tagged with any service requests (either completed or incomplete)
	Status_tagsIncomplete Status = 2 // data is tagged with service requests, one or more of which are marked incomplete
	Status_tagsComplete   Status = 3 // data is tagged with service requests, all of which are marked complete
	Status_announced      Status = 4 // tagged service requests have been announced and we are waiting for completion notification
)

func (Status) Descriptor 

func (Status) Descriptor() protoreflect.EnumDescriptor

func (Status) Enum 

func (x Status) Enum() *Status

func (Status) EnumDescriptor deprecated 

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

Deprecated: Use Status.Descriptor instead.

func (Status) Number 

func (x Status) Number() protoreflect.EnumNumber

func (Status) String 

func (x Status) String() string

func (Status) Type 

func (Status) Type() protoreflect.EnumType

Source Files

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