node

package
v2.0.0-alpha1+incompat... Latest Latest
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 Go to latest Published: Sep 17, 2019 License: BSD-2-Clause Imports: 47 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 TransitMap map[string]bool

TransitMap store UUID and bool value if object is in transit

View Source 
var TransitMapLock = sync.RWMutex{}

TransitMapLock lock write access to the CacheMap

Functions

func AsyncIndexer 

func AsyncIndexer(idxType string, nid string, colNum int, ctx context.Context)

func AzureDownload 

func AzureDownload(uuid string, nodeInstance *Node, location *conf.LocationConfig) (err error)

AzureDownload support for downloading off https://github.com/daos-stack

func DaosDownload 

func DaosDownload(uuid string, nodeInstance *Node) (err error)

DaosDownload support for downloading off https://github.com/daos-stack

func DbFindDistinct 

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

func FMOpen 

func FMOpen(filepath string) (f *os.File, err error)

FMOpen drop in replacement for os.Open that attempts to download files from locations stored in MongoDB

func GCloudStoreDownload 

func GCloudStoreDownload(uuid string, nodeInstance *Node, location *conf.LocationConfig) (err error)

GCloudStoreDownload support for downloading off https://github.com/daos-stack

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 LocationsRequest 

func LocationsRequest(ctx context.Context)

GET, PUT, DELETE: /node/{nid}/locations/{loc} , for PUT send body: {loc}, specify -H "Content-Type: application/json"

func Path2uuid 

func Path2uuid(filepath string) string

Path2uuid extract uuid from path

func ReloadFromDisk 

func ReloadFromDisk(path string) (err error)

func S3Download 

func S3Download(uuid string, nodeInstance *Node, location *conf.LocationConfig) (err error)

S3Download download a file and its indices from an S3 source

func SetFileFromParts 

func SetFileFromParts(id string, compress string, numParts int, allowEmpty bool)

this runs asynchronously and uses FileLockMgr

func ShockDownload 

func ShockDownload(uuid string, nodeInstance *Node, location *conf.LocationConfig) (err error)

ShockDownload download a file from a Shock server

func SortByteArray 

func SortByteArray(b []byte) []byte

func TSMDownload 

func TSMDownload(uuid string, nodeInstance *Node) (err error)

TSMDownload support for downloading files of an existing IBM Tivoli service

func Unzip 

func Unzip(src string, dest string) ([]string, error)

Unzip will decompress a zip archive, moving all files and folders q within the zip file (parameter 1) to an output directory (parameter 2).

Types

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"`
	Locked      *locker.LockInfo `bson:"-" json:"locked"`
}

type Indexes 

type Indexes map[string]*IdxInfo

type Location 

type Location struct {
	ID            string     `bson:"id" json:"id"`                                           // name of the location, if present data is verified to exist in said location
	Stored        bool       `bson:"stored,omitempty" json:"stored,omitempty"`               //
	RequestedDate *time.Time `bson:"requestedDate,omitempty" json:"requestedDate,omitempty"` // what is the date the data item was send on its way
}

Location a data type to represent storage locations (defined in LocationConfig) and status of data in flight

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 of Node
	Type         string            `bson:"type" json:"type"`
	Subset       Subset            `bson:"subset" json:"-"`
	Parts        *PartsList        `bson:"parts" json:"parts"`
	Locations    []Location        `bson:"locations" json:"locations"` // see below
}

func CreateNodeUpload 

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

func CreateNodesFromArchive 

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

func Load 

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

func New 

func New(uuid string) (node *Node)

func (*Node) AddLocation 

func (node *Node) AddLocation(loc Location) (err error)

AddLocation _

func (*Node) CheckTransit 

func (node *Node) CheckTransit() (locked bool)

func (*Node) DBInit 

func (node *Node) DBInit()

func (*Node) Delete 

func (node *Node) Delete() (deleted bool, err error)

Delete the node from Mongo and Disk

func (*Node) DeleteFiles 

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

DeleteFiles delete the files on disk while keeping information in Mongo FMopen will stage back the files from external Locations if requested data for nodes will subsequently be cached in PATH_CACHE not stored in PATH_DATA

func (*Node) DeleteIndex 

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

func (*Node) DeleteLocation 

func (node *Node) DeleteLocation(locID string) (err error)

DeleteLocation _

func (*Node) DeleteLocations 

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

DeleteLocations _

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) GetLocation 

func (node *Node) GetLocation(locID string) (myLocation Location, err error)

GetLocation _

func (*Node) GetLocations 

func (node *Node) GetLocations() (locations []Location)

GetLocations _

func (*Node) HasFile 

func (node *Node) HasFile() bool

has

func (*Node) HasFileLock 

func (node *Node) HasFileLock() bool

func (*Node) HasIndex 

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

func (*Node) HasIndexLock 

func (node *Node) HasIndexLock(name string) bool

func (*Node) HasParent 

func (node *Node) HasParent() bool

func (*Node) IndexFiles 

func (node *Node) IndexFiles() []string

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 file.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 file.FormFile) (err error)

func (*Node) SetFileFromPath 

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

SetFileFromPath _

func (*Node) SetFileFromSubset 

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

func (*Node) SetIndexInfo 

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

func (*Node) ToJson 

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

func (*Node) TransitLock 

func (node *Node) TransitLock()

TransitLock set info that node is in flight

func (*Node) TransitUnlock 

func (node *Node) TransitUnlock()

func (*Node) Update 

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

Modification functions

func (*Node) UpdateDataTags 

func (node *Node) UpdateDataTags(types string)

func (*Node) UpdateLinkages 

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

func (*Node) UpdateVersion 

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

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) DBInit 

func (n *Nodes) DBInit()

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
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