records

package
v0.0.0-...-e065fbe Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Mar 24, 2020 License: MIT Imports: 9 Imported by: 0

Documentation

Overview

Package records interfaces the protobuf definitions with Scribe

Package records interfaces the protobuf definitions with Scribe

Package records interfaces the protobuf definitions with Scribe

Index

Constants

This section is empty.

Variables

View Source 
var (
	// ErrNotFound is returned by operations that can't locate the required project
	ErrNotFound = errors.New("project not found")
)

error messages

View Source 
var Status_name = map[int32]string{
	0: "UN_INITIALIZED",
	1: "untagged",
	2: "tagged",
	3: "announced",
}
View Source 
var Status_value = map[string]int32{
	"UN_INITIALIZED": 0,
	"untagged":       1,
	"tagged":         2,
	"announced":      3,
}

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"`
	XXX_NoUnkeyedLiteral struct{}             `json:"-"`
	XXX_unrecognized     []byte               `json:"-"`
	XXX_sizecache        int32                `json:"-"`
}

Comments are used to record a message history

func (*Comment) Descriptor 

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

func (*Comment) GetText 

func (m *Comment) GetText() string

func (*Comment) GetTimestamp 

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

func (*Comment) ProtoMessage 

func (*Comment) ProtoMessage()

func (*Comment) Reset 

func (m *Comment) Reset()

func (*Comment) String 

func (m *Comment) String() string

func (*Comment) XXX_DiscardUnknown 

func (m *Comment) XXX_DiscardUnknown()

func (*Comment) XXX_Marshal 

func (m *Comment) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*Comment) XXX_Merge 

func (m *Comment) XXX_Merge(src proto.Message)

func (*Comment) XXX_Size 

func (m *Comment) XXX_Size() int

func (*Comment) XXX_Unmarshal 

func (m *Comment) XXX_Unmarshal(b []byte) error

type Project 

type Project struct {
	Label                string            `protobuf:"bytes,2,opt,name=label,proto3" json:"label,omitempty"`
	CID                  string            `protobuf:"bytes,3,opt,name=CID,proto3" json:"CID,omitempty"`
	Runs                 map[string]string `` /* 149-byte string literal not displayed */
	XXX_NoUnkeyedLiteral struct{}          `json:"-"`
	XXX_unrecognized     []byte            `json:"-"`
	XXX_sizecache        int32             `json:"-"`
}

Project is used to group Runs, Libraries and Samples

func InitProject 

func InitProject(label string) *Project

InitProject will init a project struct with the minimum required values

func (*Project) Descriptor 

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

func (*Project) GetCID 

func (m *Project) GetCID() string

func (*Project) GetLabel 

func (m *Project) GetLabel() string

func (*Project) GetRuns 

func (m *Project) GetRuns() map[string]string

func (*Project) ProtoMessage 

func (*Project) ProtoMessage()

func (*Project) Register 

func (project *Project) Register() error

Register will register a project on the IPFS

func (*Project) Reset 

func (m *Project) Reset()

func (*Project) String 

func (m *Project) String() string

func (*Project) XXX_DiscardUnknown 

func (m *Project) XXX_DiscardUnknown()

func (*Project) XXX_Marshal 

func (m *Project) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*Project) XXX_Merge 

func (m *Project) XXX_Merge(src proto.Message)

func (*Project) XXX_Size 

func (m *Project) XXX_Size() int

func (*Project) XXX_Unmarshal 

func (m *Project) XXX_Unmarshal(b []byte) error

type ProjectDatabase 

type ProjectDatabase struct {
	Projects             map[string]*Project `` /* 157-byte string literal not displayed */
	Pin                  bool                `protobuf:"varint,3,opt,name=pin,proto3" json:"pin,omitempty"`
	XXX_NoUnkeyedLiteral struct{}            `json:"-"`
	XXX_unrecognized     []byte              `json:"-"`
	XXX_sizecache        int32               `json:"-"`
}

ProjectDatabase is used to organise Projects

func InitDB 

func InitDB() *ProjectDatabase

InitDB will init the project database

func (*ProjectDatabase) AddProject 

func (db *ProjectDatabase) AddProject(project *Project) error

AddProject will add a project to the db

func (*ProjectDatabase) Descriptor 

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

func (*ProjectDatabase) GetNumProjects 

func (db *ProjectDatabase) GetNumProjects() int

GetNumProjects will return the number of projects in the project database

func (*ProjectDatabase) GetPin 

func (m *ProjectDatabase) GetPin() bool

func (*ProjectDatabase) GetProject 

func (db *ProjectDatabase) GetProject(projectLabel string) (*Project, error)

GetProject will get a project from the db

func (*ProjectDatabase) GetProjects 

func (m *ProjectDatabase) GetProjects() map[string]*Project

func (*ProjectDatabase) ProtoMessage 

func (*ProjectDatabase) ProtoMessage()

func (*ProjectDatabase) Pull 

func (db *ProjectDatabase) Pull(node *backend.Node, cid string) error

Pull will pull a database from the IPFS using the provided CID

func (*ProjectDatabase) Push 

func (db *ProjectDatabase) Push(node *backend.Node) (string, error)

Push will push the database to the IPFS and return the CID (and any error)

func (*ProjectDatabase) Reset 

func (m *ProjectDatabase) Reset()

func (*ProjectDatabase) String 

func (m *ProjectDatabase) String() string

func (*ProjectDatabase) XXX_DiscardUnknown 

func (m *ProjectDatabase) XXX_DiscardUnknown()

func (*ProjectDatabase) XXX_Marshal 

func (m *ProjectDatabase) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*ProjectDatabase) XXX_Merge 

func (m *ProjectDatabase) XXX_Merge(src proto.Message)

func (*ProjectDatabase) XXX_Size 

func (m *ProjectDatabase) XXX_Size() int

func (*ProjectDatabase) XXX_Unmarshal 

func (m *ProjectDatabase) XXX_Unmarshal(b []byte) error

type Run 

type Run struct {
	Created *timestamp.Timestamp `protobuf:"bytes,1,opt,name=created,proto3" json:"created,omitempty"`
	Label   string               `protobuf:"bytes,2,opt,name=label,proto3" json:"label,omitempty"`
	//string parentProjectLabel = 3;               // the label of the project that this run belongs to
	ParentProjectCID     string          `protobuf:"bytes,4,opt,name=parentProjectCID,proto3" json:"parentProjectCID,omitempty"`
	History              []*Comment      `protobuf:"bytes,5,rep,name=history,proto3" json:"history,omitempty"`
	Status               Status          `protobuf:"varint,6,opt,name=status,proto3,enum=records.Status" json:"status,omitempty"`
	Tags                 map[string]bool `` /* 150-byte string literal not displayed */
	RequestOrder         []string        `protobuf:"bytes,8,rep,name=requestOrder,proto3" json:"requestOrder,omitempty"`
	OutputDirectory      string          `protobuf:"bytes,9,opt,name=outputDirectory,proto3" json:"outputDirectory,omitempty"`
	Fast5OutputDirectory string          `protobuf:"bytes,10,opt,name=fast5OutputDirectory,proto3" json:"fast5OutputDirectory,omitempty"`
	FastqOutputDirectory string          `protobuf:"bytes,11,opt,name=fastqOutputDirectory,proto3" json:"fastqOutputDirectory,omitempty"`
	XXX_NoUnkeyedLiteral struct{}        `json:"-"`
	XXX_unrecognized     []byte          `json:"-"`
	XXX_sizecache        int32           `json:"-"`
}

Run is used to describe a Nanopore sequencing run

func InitRun 

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

InitRun will init a run struct with the minimum required values

func (*Run) AddComment 

func (run *Run) AddComment(text string) error

AddComment adds a comment to the run history

func (*Run) Descriptor 

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

func (*Run) GetCreated 

func (m *Run) GetCreated() *timestamp.Timestamp

func (*Run) GetFast5OutputDirectory 

func (m *Run) GetFast5OutputDirectory() string

func (*Run) GetFastqOutputDirectory 

func (m *Run) GetFastqOutputDirectory() string

func (*Run) GetHistory 

func (m *Run) GetHistory() []*Comment

func (*Run) GetLabel 

func (m *Run) GetLabel() string

func (*Run) GetOutputDirectory 

func (m *Run) GetOutputDirectory() string

func (*Run) GetParentProjectCID 

func (m *Run) GetParentProjectCID() string

func (*Run) GetRequestOrder 

func (m *Run) GetRequestOrder() []string

func (*Run) GetStatus 

func (m *Run) GetStatus() Status

func (*Run) GetTags 

func (m *Run) GetTags() map[string]bool

func (*Run) ProtoMessage 

func (*Run) ProtoMessage()

func (*Run) Reset 

func (m *Run) Reset()

func (*Run) String 

func (m *Run) String() string

func (*Run) Sync 

func (run *Run) Sync() error

Sync will store a run in the IPFS and update the parent project's record

func (*Run) XXX_DiscardUnknown 

func (m *Run) XXX_DiscardUnknown()

func (*Run) XXX_Marshal 

func (m *Run) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*Run) XXX_Merge 

func (m *Run) XXX_Merge(src proto.Message)

func (*Run) XXX_Size 

func (m *Run) XXX_Size() int

func (*Run) XXX_Unmarshal 

func (m *Run) XXX_Unmarshal(b []byte) error

type Sample 

type Sample struct {
	Created              *timestamp.Timestamp `protobuf:"bytes,1,opt,name=created,proto3" json:"created,omitempty"`
	Label                string               `protobuf:"bytes,2,opt,name=label,proto3" json:"label,omitempty"`
	History              []*Comment           `protobuf:"bytes,3,rep,name=history,proto3" json:"history,omitempty"`
	Status               Status               `protobuf:"varint,4,opt,name=status,proto3,enum=records.Status" json:"status,omitempty"`
	Tags                 map[string]bool      `` /* 150-byte string literal not displayed */
	RequestOrder         []string             `protobuf:"bytes,6,rep,name=requestOrder,proto3" json:"requestOrder,omitempty"`
	ParentExperiment     string               `protobuf:"bytes,7,opt,name=parentExperiment,proto3" json:"parentExperiment,omitempty"`
	Barcode              int32                `protobuf:"varint,8,opt,name=barcode,proto3" json:"barcode,omitempty"`
	XXX_NoUnkeyedLiteral struct{}             `json:"-"`
	XXX_unrecognized     []byte               `json:"-"`
	XXX_sizecache        int32                `json:"-"`
}

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

func (*Sample) Descriptor 

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

func (*Sample) GetBarcode 

func (m *Sample) GetBarcode() int32

func (*Sample) GetCreated 

func (m *Sample) GetCreated() *timestamp.Timestamp

func (*Sample) GetHistory 

func (m *Sample) GetHistory() []*Comment

func (*Sample) GetLabel 

func (m *Sample) GetLabel() string

func (*Sample) GetParentExperiment 

func (m *Sample) GetParentExperiment() string

func (*Sample) GetRequestOrder 

func (m *Sample) GetRequestOrder() []string

func (*Sample) GetStatus 

func (m *Sample) GetStatus() Status

func (*Sample) GetTags 

func (m *Sample) GetTags() map[string]bool

func (*Sample) ProtoMessage 

func (*Sample) ProtoMessage()

func (*Sample) Reset 

func (m *Sample) Reset()

func (*Sample) String 

func (m *Sample) String() string

func (*Sample) XXX_DiscardUnknown 

func (m *Sample) XXX_DiscardUnknown()

func (*Sample) XXX_Marshal 

func (m *Sample) XXX_Marshal(b []byte, deterministic bool) ([]byte, error)

func (*Sample) XXX_Merge 

func (m *Sample) XXX_Merge(src proto.Message)

func (*Sample) XXX_Size 

func (m *Sample) XXX_Size() int

func (*Sample) XXX_Unmarshal 

func (m *Sample) XXX_Unmarshal(b []byte) error

type Status 

type Status int32

Status is used to determine if experiments/samples have tagged processes, or if they have been announced via the message server 

const (
	Status_UN_INITIALIZED Status = 0
	Status_untagged       Status = 1
	Status_tagged         Status = 2
	Status_announced      Status = 3
)

func (Status) EnumDescriptor 

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

func (Status) String 

func (x Status) String() string

Source Files

View all Source files

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.