node

package
v0.9.4 Latest Latest
Warning

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

 Go to latest Published: Dec 16, 2014 License: BSD-2-Clause Imports: 24 Imported by: 14

Documentation

Index

Constants

This section is empty.

Variables

View Source 
var (
	LockMgr = NewLocker()
)

Functions

func Initialize 

func Initialize()

Initialize creates a copy of the mongodb connection and then uses that connection to create the Nodes collection in mongodb. Then, it ensures that there is a unique index on the id key in this collection, creating the index if necessary.

func IsInMappy 

func IsInMappy(item string, mp mappy) bool

func ReloadFromDisk 

func ReloadFromDisk(path string) (err error)

Types

type FormFile 

type FormFile struct {
	Name     string
	Path     string
	Checksum map[string]string
}

type FormFiles 

type FormFiles map[string]FormFile

type IdxInfo 

type IdxInfo struct {
	Type        string `bson:"index_type" json:"-"`
	TotalUnits  int64  `bson:"total_units" json:"total_units"`
	AvgUnitSize int64  `bson:"average_unit_size" json:"average_unit_size"`
	Format      string `bson:"format" json:"-"`
}

type Indexes 

type Indexes map[string]IdxInfo

type Locker 

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

func NewLocker 

func NewLocker() *Locker

func (*Locker) LockPartOp 

func (l *Locker) LockPartOp()

func (*Locker) UnlockPartOp 

func (l *Locker) UnlockPartOp()

type Node 

type Node struct {
	Id           string            `bson:"id" json:"id"`
	Version      string            `bson:"version" json:"version"`
	File         file.File         `bson:"file" json:"file"`
	Attributes   interface{}       `bson:"attributes" json:"attributes"`
	Public       bool              `bson:"public" json:"public"`
	Indexes      Indexes           `bson:"indexes" json:"indexes"`
	Acl          acl.Acl           `bson:"acl" json:"-"`
	VersionParts map[string]string `bson:"version_parts" json:"-"`
	Tags         []string          `bson:"tags" json:"tags"`
	Revisions    []Node            `bson:"revisions" json:"-"`
	Linkages     []linkage         `bson:"linkage" json:"linkages"`
	CreatedOn    time.Time         `bson:"created_on" json:"created_on"`
	LastModified time.Time         `bson:"last_modified" json:"last_modified"`
	Type         string            `bson:"type" json:"type"`
	Subset       Subset            `bson:"subset" json:"-"`
}

func CreateNodeUpload 

func CreateNodeUpload(u *user.User, params map[string]string, files FormFiles) (node *Node, err error)

func Load 

func Load(id string, u *user.User) (n *Node, err error)

func LoadFromDisk 

func LoadFromDisk(id string) (n *Node, err error)

func LoadUnauth 

func LoadUnauth(id string) (n *Node, err error)

func New 

func New() (node *Node)

func (*Node) Delete 

func (node *Node) Delete() (err error)

func (*Node) DeleteIndex added in v0.8.5 

func (node *Node) DeleteIndex(indextype string) (err error)

func (*Node) DynamicIndex added in v0.8.14 

func (node *Node) DynamicIndex(name string) (idx index.Index, err error)

func (*Node) FileExt 

func (node *Node) FileExt() string

func (*Node) FilePath 

func (node *Node) FilePath() string

func (*Node) FileReader 

func (node *Node) FileReader() (reader file.ReaderAt, err error)

func (*Node) HasFile 

func (node *Node) HasFile() bool

has

func (*Node) HasIndex 

func (node *Node) HasIndex(index string) bool

func (*Node) HasParent 

func (node *Node) HasParent() bool

func (*Node) IndexPath 

func (node *Node) IndexPath() string

func (*Node) Mkdir 

func (node *Node) Mkdir() (err error)

func (*Node) Path 

func (node *Node) Path() string

path

func (*Node) Rmdir 

func (node *Node) Rmdir() (err error)

func (*Node) Save 

func (node *Node) Save() (err error)

func (*Node) SetAttributes 

func (node *Node) SetAttributes(attr FormFile) (err error)

func (*Node) SetAttributesFromString added in v0.8.5 

func (node *Node) SetAttributesFromString(attributes string) (err error)

func (*Node) SetFile 

func (node *Node) SetFile(file FormFile) (err error)

func (*Node) SetFileFormat 

func (node *Node) SetFileFormat(format string) (err error)

func (*Node) SetFileFromParts 

func (node *Node) SetFileFromParts(p *partsList, allowEmpty bool) (err error)

func (*Node) SetFileFromPath 

func (node *Node) SetFileFromPath(path string, action string) (err error)

func (*Node) SetFileFromSubset added in v0.8.12 

func (node *Node) SetFileFromSubset(subsetIndices FormFile) (err error)

func (*Node) SetIndexInfo 

func (node *Node) SetIndexInfo(indextype string, idxinfo IdxInfo) (err error)

func (*Node) ToJson 

func (node *Node) ToJson() (s string, err error)

func (*Node) Update 

func (node *Node) Update(params map[string]string, files FormFiles) (err error)

Modification functions

func (*Node) UpdateDataTags 

func (node *Node) UpdateDataTags(types string) (err error)

func (*Node) UpdateLinkages 

func (node *Node) UpdateLinkages(ltype string, ids string, operation string) (err error)

func (*Node) UpdateVersion 

func (node *Node) UpdateVersion() (err error)

type Nodes 

type Nodes []*Node

Node array type

func LoadNodes 

func LoadNodes(ids []string) (n Nodes, err error)

func (*Nodes) GetAll 

func (n *Nodes) GetAll(q bson.M) (err error)

func (*Nodes) GetPaginated 

func (n *Nodes) GetPaginated(q bson.M, limit int, offset int) (count int, err error)

type Parent added in v0.8.12 

type Parent struct {
	Id        string `bson:"id" json:"-"`
	IndexName string `bson:"index_name" json:"-"`
}

type Subset added in v0.8.12 

type Subset struct {
	Parent Parent            `bson:"parent" json:"-"`
	Index  SubsetNodeIdxInfo `bson:"index" json:"-"`
}

Subset is used to store information about a subset node's parent and its index. A subset node's index defines the subset of the data file that this node represents. A subset node's index is immutable after it is defined.

type SubsetNodeIdxInfo added in v0.8.13 

type SubsetNodeIdxInfo struct {
	Path        string `bson:"path" json:"-"`
	TotalUnits  int64  `bson:"total_units" json:"-"`
	AvgUnitSize int64  `bson:"average_unit_size" json:"-"`
	Format      string `bson:"format" json:"-"`
}

Source Files

View all Source files

Directories

Path Synopsis
Package contains Node File struct and MultiReaderAt implementation
 Package contains Node File struct and MultiReaderAt implementation
format/fasta
Package to read and write FASTA format files
 Package to read and write FASTA format files
format/fastq
Package to read and write FASTQ format files
 Package to read and write FASTQ format files
format/line
Package to read and index lines of a file
 Package to read and index lines of a file
format/multi
Package to read and auto-detect format of fasta & fastq files
 Package to read and auto-detect format of fasta & fastq files
format/sam
Package to read and write SAM format files
 Package to read and write SAM format files
format/seq
Package contains interfaces for fasta & fastq & and multi packages
 Package contains interfaces for fasta & fastq & and multi packages
index
anonymize
fq2fa

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.