node

package
v0.9.21 Latest Latest
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This package is not in the latest version of its module.

 Go to latest Published: Apr 13, 2017 License: BSD-2-Clause Imports: 29 Imported by: 0

Documentation

Index

Constants

This section is empty.

Variables

View Source 
var DocumentMaxByte = 16777216

mongodb has hard limit of 16 MB docuemnt size

View Source 
var (
	LockMgr = NewLocker()
)

Functions

func DbFindDistinct 

func DbFindDistinct(q bson.M, d string) (results interface{}, err error)

func HasAttributeField 

func HasAttributeField(a string) bool

func InitReaper 

func InitReaper()

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)

func RemoveAllFormFiles 

func RemoveAllFormFiles(formfiles FormFiles)

func SortByteArray 

func SortByteArray(b []byte) []byte

Types

type FormFile 

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

func (*FormFile) Remove 

func (formfile *FormFile) Remove()

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:"-"`
	CreatedOn   time.Time `bson:"created_on" json:"created_on"`
}

type Indexes 

type Indexes map[string]IdxInfo

type Locker 

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

func NewLocker 

func NewLocker() *Locker

func (*Locker) AddNode 

func (l *Locker) AddNode(id string)

func (*Locker) GetNodes 

func (l *Locker) GetNodes() (ids []string)

func (*Locker) LockNode 

func (l *Locker) LockNode(id string)

func (*Locker) RemoveNode 

func (l *Locker) RemoveNode(id string)

func (*Locker) UnlockNode 

func (l *Locker) UnlockNode(id string)

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"`
	Indexes      Indexes           `bson:"indexes" json:"indexes"`
	Acl          acl.Acl           `bson:"acl" json:"-"`
	VersionParts map[string]string `bson:"version_parts" json:"version_parts"`
	Tags         []string          `bson:"tags" json:"tags"`
	Revisions    []Node            `bson:"revisions" json:"-"`
	Linkages     []linkage         `bson:"linkage" json:"linkage"`
	Priority     int               `bson:"priority" json:"priority"`
	CreatedOn    time.Time         `bson:"created_on" json:"created_on"`
	LastModified time.Time         `bson:"last_modified" json:"last_modified"`
	Expiration   time.Time         `bson:"expiration" json:"expiration"` // 0 means no expiration
	Type         string            `bson:"type" json:"type"`
	Subset       Subset            `bson:"subset" json:"-"`
	Parts        *PartsList        `bson:"parts" json:"parts"`
}

func CreateNodeUpload 

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

func CreateNodesFromArchive 

func CreateNodesFromArchive(u *user.User, params map[string]string, files FormFiles, archiveId string) (nodes []*Node, err error)

func Load 

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

func New 

func New() (node *Node)

func (*Node) ClearRevisions 

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

func (*Node) Delete 

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

func (*Node) DeleteIndex 

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

func (*Node) DynamicIndex 

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) RemoveExpiration 

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

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 

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

func (*Node) SetExpiration 

func (node *Node) SetExpiration(expire 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(allowEmpty bool) (err error)

func (*Node) SetFileFromPath 

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

func (*Node) SetFileFromSubset 

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

func (*Node) SetIndexInfo 

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

func (*Node) SetPriority 

func (node *Node) SetPriority(priority int) (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 NodeLock 

type NodeLock struct {
	sync.Mutex
}

type NodeReaper 

type NodeReaper struct{}
var (
	Ttl         *NodeReaper
	ExpireRegex = regexp.MustCompile(`^(\d+)(M|H|D)$`)
)

func NewNodeReaper 

func NewNodeReaper() *NodeReaper

func (*NodeReaper) Handle 

func (nr *NodeReaper) Handle()

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, order string) (count int, err error)

type Parent 

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

type PartsList 

type PartsList struct {
	Count       int         `bson:"count" json:"count"`
	Length      int         `bson:"length" json:"length"`
	VarLen      bool        `bson:"varlen" json:"varlen"`
	Parts       []partsFile `bson:"parts" json:"parts"`
	Compression string      `bson:"compression" json:"compression"`
}

type Subset 

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 

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
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